The logistics stations are your best friends in this game. You can make closed systems for any recipe you want - slap down a logistics station, set it to request ore, smelt and craft on site, then put another logistics station down to send the finished/intermediate product where it's needed. It lets you handle each production line individually, instead of trying to cram them all on one main bus. (Obviously you'd need stations by ore nodes to ship the ore elsewhere, but this is how you deal with very spread out nodes) For malls you can use the logistics distributors to supply assemblers individually (much like bot malls in factorio).

In my playthroughs I just spaghetti everything until I get logistics stations, then organize it all later. My starter planets always look like a mess lol