I went to all of the trouble of creating a forestry farm to produce the Blue Mahoe trees so that I had plenty of saplings for biofuel. In hindsight, I had that many normal saplings, that I could have just burned them up instead.
I've nearly finished all of the go with the flow quests, the only hang up is the liquid protein. To do that one, you really need a spawner and a slaughter house, using conventional breeding just isn't fast enough.
For bees, I really recommend using the Gendustry machines, work out which bees have desirable traits, specifically you want the high fertility, none effect (or beneficial effect of your choice), flowers pollination, the tolerance as best you can, and then for breeders, shortest life, and for producers, fastest production.
Then using industrial apiaries, use either production upgrades for your producers, or lifespan upgrades for your breeders. I ended up with that many princesses for forest and medows that I was burning them for liquid DNA.