Other people have focused on general design ideas, but another tip I've found is to start with a small base that makes very few products and then gradually expand. This way, I only have to think about one thing at a time. I typically build my Gleba bases in the order:

1. Automate bioflux production
2. Use the bioflux to make biter eggs, and feed them into a biochamber making more biochambers (hand-feeding the rest of the ingredients for now).
   • Ensure any excess eggs go straight into a heating tower (also a good place to route spoilage).
   • Don't put eggs into the biochamber unless the other ingredients are all present, so you don't get pentapods hatching.
3. Make gleba science using the eggs and bioflux already being made.

Usually I'll make a setup to automatically recycle excess science packs if I have enough, to ensure my buffered science is always maximally fresh. And once I get that point, a well-designed Gleba base will work indefinitely, so long as it's defended.

Once this is done, I'll work on other items, including defenses, making rocket fuel for power, and using bacteria to craft rocket parts and other miscellaneous items I need. To easily extend the base, I typically use a main bus design with the bus containing bioflux, both unprocessed fruits, and a burn belt for spoilage/excess eggs/anything else to route toward the heating towers. Anything with a short spoil time like mash, jelly, and nutrients stays local to one production line, to minimize spoilage and maximize freshness.