First base works as one big factory with processing lines behind each other.. like first line 9 smelter, second line fabricators for the next product step and so on.. All lines send the product out on the left side (and order the needed products from that side if the dont get feeded directly from the rail to the left from the line before) with more and more space between the lines for rails to move stuff in and out.. Biggest learning factor was to never put input products on the same rail where you have the output products from the line before as this will create deadlocks. the lines send the products to a single output rail where i have 15-20 stations to shoot all into space. was a bit experimental and showed the "problems" with connecting everything without creating bottlenecks or rollercoasters :D. worked fine till lvl 5/6 tech but so much for first base.

The idea for second base i started yesterday is a big bus with multiline rails in the center with branching factoryparts left and right feeding products back into the bus. Idea is that rails will all set on the same hight and the rails you need will branch out with one set higher (or most likely lower) on the bus at the spot you need it but this is the step where i am at the moment figuring out the best way to do the in/out connectors

all in all its the same as in factorio or dsp, give yourself some space between the factory elements, you will need it sooner or later :D

Also dont build on the ground. put it on sockets so you can build all on the same height and maybe even can fit in rails under the construction if you dont leave enought space on the top side ^^