It's simple: first you look for any resource you need, then you see if any bee can make that resource, then you feed tons of uranium or redstone to Gendustry's liquid mutation thing maker, then you use that to reliably progress through the bee breeding chain until you get to that bee you want (probably twice because I don't remeber if you get a queen or princess/drone out of Gendustry's setup). Lastly, you set up an industrial apiary with the automation upgrade and any other upgrades you want (look at the mod's website to see your options), feed it enough energy, and forget about it while enjoying your infinite resources. Unless you got the kind of bee that dies, I forgot if it's ignoble or pristine, because Sengir hates fun. I guess you can feed the extra drones to that machine that separates traits or species I don't know because you most likely won't need them.
The other options to get to a certain bee involve either way too much randomness or even more randomness at a lower chance of getting what you want, so I don't bother with them anymore.
tl;dr You will either love them or hate them, but because of some bias I'd say you're more likely to hate them.
Ignoble Bees tend to die after a few generations.
I "suggest" you get the Nether Simulator upgrade, the Internal Lighting upgrade, Waterproofing Upgrade, and there is one more(it is the one that Internal Lighting isn't, so if Internal Lighting makes it always day, get the one that makes Caves OK for all bees as well) that I "suggest" you get. Oh, and Automation, but that's an Obvious "Suggestion".
I can only "Suggest" these upgrades, because they are truly needed upgrades. The fact that there is a Nether Simulator is amazing, as it allows you to breed Bees that must be bred in the Nether, anywhere. There are of course upgrades to make it Hotter, Dryer, Wetter, and/or Colder, which help getting bees to work(indeed, it can even get them to produce specialty stuff I think, literally anywhere), and production increasing upgrades, ones that make bees have bigger teritory, one that does something to their lifespan(that I don't quite understand), and many other useful things, but those ones I named before? All but essential for 24/7 Bee Keeping able to match a Alveary in customization, utility, and output.
If you don't mind feeding some power to a Apiary to make it as good(really, actually better) then a Alveary, use Gendustry's Fancy Apiary. If you don't mind waiting until you are late in the Beekeeping Game to have a bunch of useful Alvearies that don't work as a Nether subsitute, but don't need power, use Extra Bees Alveary blocks.
Either way, you should have them both installed. Extra Bees has Extra Bees(no shit!), but also it's BinniesMods, which includes Extra Trees(and it adds EXTRA KINDS OF TREES TO BREED! Oh and some awesome Treekeeping stuff, namely a block that mixes your wood and makes it look awesome), Gendustry has better Bee Breeding junk, and has a Powered Grafter, which is all kinds of awesome, supports RF natively, and is at least 20% cooler over all I'd say.
Also, if you have enough bee breeds to breed(hint: You don't. Period.), you may not be Interested in Magic Bees, which adds all kinds of more Magical Bees, which tend to produce things for mods like Thaumcraft, EE3, AM1/2, TE3, and other bees that are useful(such as a bee that allows you to make Wither Skulls, or one that makes Dragon Eggs), and a bunch of cool things that are semi-broken OP(a frame called the Oblivion Frame, which makes bees die instantly when you use it in a apiary, but it is awesome for breeding bees, for a example).
All in all, if you don't mind a bit of work(or tedium as some might call it), Beekeeping is a very lucrative way to make all kinds of useful things.
Also, there is a upgrade for MMPS that makes your armor double as an apiarist suit. Suck THAT, crappy Apiarist Suit!
