Ideally you hit that point right around the time you launch your first rocket, so when you start your second factory you have a much better idea of how to approach things and it's much easier with a completely clean slate. Or at least that's how it went for me.

My first factory was complete spaghetti. A couple haphazard rail lines, conveyor belts going everywhere, a veritable labyrinth of pipes to deal with all the oil and little construction outposts scattered all over with no rhyme or reason.

When I moved on to the second factory I had everything all in a big line scrunched together with construction peeling off from the main resource belt. I only kept that thing functional long enough to get trains up and running and from there I built a whole railway empire. Big orderly blocks of train based input and output. Every square a function with parameters and outputs all feeding into one another. It was beautiful.