You need more Princesses as the breeding process goes on because you can't breed Drones together, so you will need to set up more Apiarys.
Now that you have bred some Common and some Cultivated bees, you want to be able to make this whole breeding process simpler and more customisable. You may have seen some bees that simply will not work in the biome of your “bee Base”.
The Alveary will come in handy with this. Not only will you be able to change the temperature, but you can breed almost any bee. It's basically endgame when it comes to Forestry breeding tools. It is very expensive to make, and does require you to breed certain bees.