I've played the game through about three times now, and here's the two major things that get me through it:

1. Modularity. I built a lot of things in standard 10x10 blocks I could quickly spam out with the SMART mod, and using that as a basic building block I would build production lines and whole factories. 4 modules of smelters, 4 modules of constructors, 2 modules of assemblers and 2 modules of manufacturers and you've gone from raw ore to computers or something. This approach is extensible, you can quickly bang out a production line, get some of it going, then widen it in parallel to increase throughput as demand increases.

2. Step by step. When I stop to think about how my whole world-circling megafactory works, it's kind of overwhelming. I don't think I could have sat down and designed it from the top down. But "This factory mines iron and copper on site, gets plastic from the train network, makes circuit boards and computers, and then sends them out the train network" is easier to manage. As you build a step in the process, stop considering the rest of the world, think "this will get ingredients from somewhere and will sent products to somewhere else."