Not basic stuff at all. You're asking good questions off the beaten path.
While not a virtual machine, I can see how Wine has that feel. Especially if you've used Unity mode in VMWare Workstation, or something similar, where there's an option to have guest applications "appear" to run outside their little window.
Getting a Windows game into Lutris can happen two ways. Easiest is installing via Lutris installer, if your game is not too obscure. For obvious reasons, the installer will only have hooks for official retail setup files, so under a black flag, things get trickier. Even then, still check out the Lutris installer to easily see if there are recommended patches and fixes.
If you just have a setup.exe, there's a "install a windows game from executable" that works mostly like the Lutris installer except you will have to give it a name and which version of Windows Wine will try to work like. Like the Lutris installer, this will also give you a path to where all the stuff is installed.
You might also have just a bunch of files, no installer or setup.exe. This is a bit harder still but not too awful. Unzip it someplace, use the "add a locally installed game" option, and select Wine as your runner. The defaults are usually pretty sensible, but I certainly haven't tried every game ever made.
Rest of the setup: Working directory is implied to be where the main executable is, so don't mess with it. Don't set up arguments unless you know you need them: these go to the GAME not the runner. Wine prefix sets up a Wine sandbox of sorts, what you observe feels like a VM. You could just one use, but MB are cheap these days, I just use a separate prefix for each game, and I just use the directory where the game is installed. If it doesn't work right away, scan down the list of runner options and see what might be sensible.
"Where do I drop files?"
Once you've got the game installed, and perhaps run it to check, check the Wine prefix directory. It'll look something like this: https://files.catbox.moe/sfug25.png (pardon the censoring, but you understand). From there you have a directory that is your "fake" C: drive. If you keep a separate prefix for every game, you also don't need to be particularly hygenic here. Installing to the "fake C: root" is just fine, there's no real advantage to using Program Files.
Using a mod manager? Copy that in to your wine prefix. (Not strictly required, but I'd recommend it). Then hit the second collapsible menu on the Lutris UI, corresponding to Wine options, and "Run EXE inside Wine prefix". It will automatically open a file picker, to the directory where your prefix is, and it will run it in that sandboxed environment.
If you are using your mod manager a lot, you have a few quality of life things you can do. If the manager launches the game, just go into the game's configuration in Lutris and set the mod manager exe as the executable instead of the game proper. If not, you might want to consider Duplicating the game and changing the executable of one of the copies to the mod manager. Using Duplicate will have both the "games" (really, one game and a supplement) pointing to the same prefix so they're in the same sandbox.
"How do you organize your files / multiple hard disks / conventions"
That's a very personal question for sure: I have a system that works for me and make no warranties that it will work for anyone else. It also has limitations, for sure, but I see it as those four junk drawers in my house full of random shit but I know exactly which one I need to get into when I need to find a 20 year old ticket stub. I have a central NAS where I save most of my files, so each computer has a "local stuff" and a "network stuff" folder. On my final Windows 7 machine, it's a permanent network mount at a letter, and a directory link to that network mount. On my Linux machines I fstab entries, which was a pain in the ass to get working right and would definitely piss you off. Still, stick with it and it's one of those things that stays solved once you solve it, and you'll never have to look at it again.
In both cases, I have a pretty loose divide between stuff I made, stuff I converted, and stuff I downloaded. From there it's really anything goes. I bought Old School Essentials a while ago, and I had all the pdfs on a local computer's "Downloads/Reading/Games/RPG/". Then I have a script to move stuff from local machines onto the NAS. Sometimes automatic, sometimes manual, depending on how often I'm accessing it. Sometimes I'll manually copy things over if it's slow over the network to work with.
Multiple hard disks? I don't do that anymore, so this is coming from blind memory. Modern linux will automatically mount internal disks "somewhere" and make an icon available but the file browser will tell you where if you need a path by right clicking and picking properties. You can have more control by using fstab but, again, a pain in the butt because if you don't pay attention you can break shit.
.
With enough experience and time, you'll come up with the ways you're comfortable doing things which will be different from above. But hopefully this is enough to get started.
I don't have an answer for Windows -> Linux, precisely. I've never tried moving a game in progress from one to the other. Files? Central NAS means I never had to go from desktop to desktop. Running TrueNAS [Core] on that machine, so that's a third operating system that is more server focused and, frankly, I don't do anything there that isn't out of the box functionality.
If someone put a gun to my head, I'd probably set up a Windows share, then use the Linux file manager (gnome, is what I use, in case it comes up) to mount that share and copy. I'm sure the other way works as well, I'm just personally more familiar with setting up Windows shares because it's easy to just give the Everybody role access to everything and it works without any fuss over my local network, whereas for Linux you can't really get away without needing some kind of credentialed user for network file sharing.
Not basic stuff at all. You're asking good questions off the beaten path.
While not a virtual machine, I can see how Wine has that feel. Especially if you've used Unity mode in VMWare Workstation, or something similar, where there's an option to have guest applications "appear" to run outside their little window.
Getting a Windows game into Lutris can happen two ways. Easiest is installing via Lutris installer, if your game is not too obscure. For obvious reasons, the installer will only have hooks for official retail setup files, so under a black flag, things get trickier. Even then, still check out the Lutris installer to easily see if there are recommended patches and fixes.
If you just have a setup.exe, there's a "install a windows game from executable" that works mostly like the Lutris installer except you will have to give it a name and which version of Windows Wine will try to work like. Like the Lutris installer, this will also give you a path to where all the stuff is installed.
You might also have just a bunch of files, no installer or setup.exe. This is a bit harder still but not too awful. Unzip it someplace, use the "add a locally installed game" option, and select Wine as your runner. The defaults are usually pretty sensible, but I certainly haven't tried every game ever made.
Rest of the setup: Working directory is implied to be where the main executable is, so don't mess with it. Don't set up arguments unless you know you need them: these go to the GAME not the runner. Wine prefix sets up a Wine sandbox of sorts, what you observe feels like a VM. You could just one use, but MB are cheap these days, I just use a separate prefix for each game, and I just use the directory where the game is installed. If it doesn't work right away, scan down the list of runner options and see what might be sensible.
"Where do I drop files?"
Once you've got the game installed, and perhaps run it to check, check the Wine prefix directory. It'll look something like this: https://files.catbox.moe/sfug25.png (pardon the censoring, but you understand). From there you have a directory that is your "fake" C: drive. If you keep a separate prefix for every game, you also don't need to be particularly hygenic here. Installing to the "fake C: root" is just fine, there's no real advantage to using Program Files.
Using a mod manager? Copy that in to your wine prefix. (Not strictly required, but I'd recommend it). Then hit the second collapsible menu on the Lutris UI, corresponding to Wine options, and "Run EXE inside Wine prefix". It will automatically open a file picker, to the directory where your prefix is, and it will run it in that sandboxed environment.
If you are using your mod manager a lot, you have a few quality of life things you can do. If the manager launches the game, just go into the game's configuration in Lutris and set the mod manager exe as the executable instead of the game proper. If not, you might want to consider Duplicating the game and changing the executable of one of the copies to the mod manager. Using Duplicate will have both the "games" (really, one game and a supplement) pointing to the same prefix so they're in the same sandbox.
"How do you organize your files / multiple hard disks / conventions"
That's a very personal question for sure: I have a system that works for me and make no warranties that it will work for anyone else. It also has limitations, for sure, but I see it as those four junk drawers in my house full of random shit but I know exactly which one I need to get into when I need to find a 20 year old ticket stub. I have a central NAS where I save most of my files, so each computer has a "local stuff" and a "network stuff" folder. On my final Windows 7 machine, it's a permanent network mount at a letter, and a directory link to that network mount. On my Linux machines I fstab entries, which was a pain in the ass to get working right and would definitely piss you off. Still, stick with it and it's one of those things that stays solved once you solve it, and you'll never have to look at it again.
In both cases, I have a pretty loose divide between stuff I made, stuff I converted, and stuff I downloaded. From there it's really anything goes. I bought Old School Essentials a while ago, and I had all the pdfs on a local computer's "Downloads/Reading/Games/RPG/". Then I have a script to move stuff from local machines onto the NAS. Sometimes automatic, sometimes manual, depending on how often I'm accessing it. Sometimes I'll manually copy things over if it's slow over the network to work with.
Multiple hard disks? I don't do that anymore, so this is coming from blind memory. Modern linux will automatically mount internal disks "somewhere" and make an icon available but the file browser will tell you where if you need a path by right clicking and picking properties. You can have more control by using fstab but, again, a pain in the butt because if you don't pay attention you can break shit.
.
With enough experience and time, you'll come up with the ways you're comfortable doing things which will be different from above. But hopefully this is enough to get started.
I don't have an answer for Windows -> Linux, precisely. I've never tried moving a game in progress from one to the other. Files? Central NAS means I never had to go from desktop to desktop. Running TrueNAS [Core] on that machine, so that's a third operating system that is more server focused and, frankly, I don't do anything there that isn't out of the box functionality.
If someone put a gun to my head, I'd probably set up a Windows share, then use the Linux file manager (gnome, is what I use, in case it comes up) to mount that share and copy. I'm sure the other way works as well, I'm just personally more familiar with setting up Windows shares because it's easy to just give the Everybody role access to everything and it works without any fuss over my local network, whereas for Linux you can't really get away without needing some kind of credentialed user for network file sharing.