SpaceChem is pretty much the same thing as Opus Magnum and MOLEK-SYNTEZ... but different! Helpful description, right?

The big difference is that you are going to be operating at multiple levels. The outside, connecting up the reactors part is pretty simple but deceptively so. All you have to do is click and drag the out's to the in's so that the ingredients enter the reactor for combination and the results get to the barges.

Simple enough

But! (There it is) You need to be careful about timing. Backups in the exit flow may throw off your production rhythm as products wait to exit. Long travel times from one supply tank relative to another may result in one line starting its processing much sooner than the other one. Thank Zach for the Sync command!

Once you have your mechanisms set, you can watch from above in a godlike POV as the ingredients enter the reactors that operate in miniature. You can follow the entire process in this manner and see that plan come together. Cue cigar.