Now that you have imperial bees, if you want to advance further in beekeeping the advanced genetic machines allow access to an easier mutation method.
Build the genepool first, if you haven't already. Rig up an apiary with max fertility bees to automatically breed and breed and breed, and every time you get a full stack of 64 drones, beealyse it (you can do the whole stack with a single bit of honey) and throw it in the genepool.
Next build an isolator, synthesiser, purifier and inoculator. These each require an advanced genetic machine each as part of their construction. Rig up a waterproof pipe system to go from the genepool to the synthesiser and purifier.
Note that all these machine chew up MJ (Buildcraft power). They'll do this whether they're in use or not, so make sure you rig the system so's you can easily disable their power supply when they're no in use.
They're simple enough to use; empty serum vials (made using royal jelly from the imperial bees, along with a few other things) go in the isolator along with some drones. Random serums come out, each set to a specific trait from those drones. This occasionally kills the bees, so don't put anything important in (eg princesses) in.
To start with, concentrate on getting shortest lifespan and maximum fertility serums. Once you have either of those two, throw them into the synthesiser. This will start to charge the serums - they go up to 16 uses tops. After this put the serums in the purifier and leave them there until it gives a red warning symbol telling you it can't improve them further.
Finally, bees you want to alter go in the inoculator along with the finished serums. Each charge that is applied randomly affects either the active or inactive traits on the bees.
Empty serums can be put back into the synthesiser, but remember to put them in the purifier after that - even if they still appear to be top quality. Unwanted serums can go through the furnace to revert them to empty so they can go back in the isolator.
Now, how all this relates to breeding: Take a princess and drone each of your two parent species, and fully inoculate them with the maximum fertility and shortest lifespan traits (on average you'll use 3 charges per bee, but it's best to budget for 4 - the serums will be mostly empty by the time you've done four bees).
Allow these two bees to breed a few times to build up a stack of identical drones. At this point you should throw away any other remaining drones you have of these species (if they don't stack then don't bother putting them in the genepool; it's faster to only use stacking drones there). If you have any princesses of these species then breed them with the stacks you just made so that they get the new traits too.
Now when you go to mutate, you'll be spending a lot less time at the hives. Princess goes in with a drone stack and some soul frames. Lots of drones come out. Throw away any drones that lack the new traits you want. Throw any drones that DO get the new traits you want in the isolator. Depending on what sort of princess you get out, switch the drone stack with each breeding cycle. Keep your serums charged in case the princess loses its fertility via mutation and keep going until you have the serums you want.
Sometimes you'll "naturally" breed through to a pure princess and drone before the isolator gets the race trait for you. That's fine, but it's often worth getting the serum anyway: because you have already have stacks of drones with maximum fertility and shortest lifespan, it's easy to clone princesses by breeding them with that stack. You then take the princess and one of those drones and inoculate it with your new race, and hey presto! Unlike with the mutation system, which would've knocked all the decent traits off the parent drones, racial inoculation leaves all other traits intact - you've now got pure bees of a new species that are still fully fertile and don't take forever to die. And if the new species was outright dangerous (eg, radioactive bees have the "unstable" effect which can do you a whole lot of damage), then you've also just saved yourself the time of inoculating that out of them.
Every time you come across a new trait you like (eg "fast production" from cultivated, "fast pollination" from industrious, "explorer" from edenic, etc), produce a new drone stack that incorporates it and throw away all the others.