Also, make an apiarist database as soon as you can along with the acclimatizer. Even though this is a tier 1 bee machine, it can fix the temperature and humidity tolerances of your bees. This is often needed while breeding and you get a bee that won't work in your current climate because a mutation caused your temp or humidity tolerances to be lost. The apiarist database is good to see what the base traits are on a bee so you can see what you try and need to save with your breeding. Sometime you only want the species and don't care about the traits (cause you have better bred bees already), other times you want the traits. (like the fast worker from cultivated.) Occasionally, I've gotten mutations where the trait I wanted doesn't actually end up on the bee, even though it is a base trait. (I see this happen most often in double mutations--both active and inactive strains mutate.) When this happens, I have to try again with the mutation.
One of the tricks I've found when manually breeding the 1x offspring bees is to have a princess with a 4x fertility and a purebred drone with the 1x fertility. Then you end up with a bunch of bees that are hybrids with 1x fertility as the active trait and hopefully a 4x inactive. I save all the drones from this mating. Next, I breed 4x fertility back into the princess and hopefully save a couple traits from the 1x fertility bee. Next, I breed one of the drones from the first mating with the fixed 4x fertility princess. I save all the drones from this second pairing as well. If I lose the 4x fertility, I breed it back in from the source strain. If not, I try and purify/stabilize the bee line with just the one drone. Once I have the stable pair, I clone the princess, then take another drone from my first couple breedings and mate with this new princess. If I lose the 4x fertility, I go back to my first mating princess and use the drones to fix the second mating princess. Once the second mating princess becomes stable, I will incorporate the traits from the first back in if need be, then this new mating princess becomes the baseline for the new bees. I then clone the second mating princess back to the first, then breed it again with a bee from the original couple pairings, going for any traits that got lost along the way. Occasionally, these pairings have bad luck, and I have to revert back to my stable mating pair. Even though it takes a while to stabilize and clone the breeding pairs, it is worth it when manually breeding the 1x species.
Always have one line is stable and producing drones for you to go back to when the RNG is being evil. Only work on a few traits at a time. Go for as many as possible, but stabilize the line, first and foremost. Then, clone the stable line, and start trying to add in the traits you want, and breed in drones from the stable line as needed to repair lost traits and what not. I've done this and got lucky bringing in 3 or 4 good traits, other times, I've had horrible luck and lost all my progress on the new line and had to go back and clone the stable line again.
Once you get imperial and industrial, it is only a matter of time before you breed all the bees you want. The escritore can work with bee products, but also with the bees themselves. It's a good use of the stacks and stacks of drones you make. You can use all the hybrids to research. Only the dominant species is used for the escritore.