If you want to understand bee breeding you need to understand several things:
Traits
The bee genome gives the bees a number of traits. The foremost of these, is the species trait. (This trait is ridiculous as the species of a creature is actually the emergent property of all its other traits). Nonetheless, in Forestry, the species trait gives the bee its name, its product (strangely, unrelated to the flowers the bee forages), and its base Humidty and Climate temperature preference.
Other traits are:
* Lifespan (Shortest, Shorter, Short, Shortened, Normal, Elongated, Long, Longer, Longest). You want the shortest lifespan on bees you are breeding for quick turnaround, and longest on your production bees, to cut down on the drone buildup.
* Speed (Slowest, Slower, Slow, Normal, Fast, Faster, Fastest) How quickly the bees produce their output. Fastest is best.
* Flowering (Slowest, Slower, Slow, Average, Fast, Faster, Fastest, Maximum) How quickly the bees produce flowers, and also how often they mutate nearby leaf blocks by carrying pollen around.
* Flowers (various) What kind of flowers the bee needs to have in range of the hive to operate. Also, certain flower types will be spawned near the hive. "End" means dragon egg, "Nether" means netherwart (iirc), everything else is obvious.
* Fertility (1...4) how many drones the Queen will make when she dies. While breeding bees you need to watch the fertility because the lower it is the greater the chance that you will loose traits you are breeding for.
* Territory (Nnormal (9x6x9), Large (11x8x11), Larger (13x12x13), Largest(15x13,15) - the size of the area centered around a apairy in which a bee must find its flower. The bees actual range for mutating blocks, and spawning flowers, is 3x this. An Alveary extends the territory again by a factor of 3x? This also is the range that the bees effect is applied too.
* Effect. (none / various). Bees have a variety of effects. Some are beneficial, some damage you. The damaging effects can all be mitigated by wearing an Apiarists suit. Of note is 'reanimation' that can crash a server if used near skeletons as it will reanimate dropped bones into skeletons, which if killed, drop more bones. Reanimation does NOT reanimate the ender dragon from a dragon egg.
* Temperature Tolerance, (None, Up_x, Down_x, Both_x, x=1...4) How many points away from the bees base temperature (Climate) the bee will tolerate working.
* Humidity Tolerance (None, Up_x, Down_x, Both_x, x=1..2) How many points away from the bees base humidity (Humidity) the bee will tolerate working.
* Nocturnal: (yes/no) can the bee operate at night.
* Flyer (yes/no) can the bee operate during weather (in biomes where weather manifests)
* Cave (yes/no) does the bee require the hive to have an unobstructed view of the sky to work.
"Fake" traits (Dirunal is not a choice but some tools show it, Humidity and Climate are determined by the species)
* Dirunal - (yes) all bees can operate during the day
* Humidity (Arid, Normal, Damp) How dry the biome must be for the bee to work.
* Climate (Icy, Cold, Normal, Hot, Hellish) What temperature the biome must be for the bee to work.
Allels & Dominant vs Recessive
Bees have two copies of each trait, called Allels, and the dominant trait is the one that will manifest on the bee. The danger here is that, while breeding bees for a purpose, important traits - such as the species - might be recessive and thus not visible.
Beyond that, Ignore any advice that talks about dominant vs recessive traits in Forestry Bees. This topic is entirely irrelevant as the only sane way to deal with bees is in stacks, and the only way to get stacks of drones, is when the two alleles for each trait are identical. Also, the dominance or recessiveness of a allel in no way determines its selection during breeding. Each allel for each trait has a 50% chance of being picked.
Do note that, the production of a new species is NOT traditional genetics. What seems to happen is, if the conditions for a mutation to a new species are met, the Queen will produce an offspring with one COMPLETE set of its allels replaced with the "default" for this new species. So, even if you are breeding with a queen created from a princess with Fertility:4,4 and a drone with Fertility:4,4, if the result is a secluded bee, its the new secluded bee will have Fertility:1,4.
Your desired Progression
Starting with Hive bees, you are going to want to find and breed:
* Find Jungle bees - to start making silk wisps.
* Find Medows and Forest bees
* Common, Cultivated from Hive Bees.
* Noble, Magestic, Imperial, to produce Royal Jelly
* Diligent, Unweary, Industrious, to produce Pollen
You should have enough bees now to produce honey, beeswax, pollen and royal jelly, which you will need lots of to build alvearies. The silk wisps you will produce from the Tropical (watch out) bees will be necessary to make the apiarists suit that will protect you from the damage done by the nether bees that are pretty much the gateway to the rest of the interesting bees.
Quite a lot of that honey is also going to go to powering the beealyzer that is absolutely crucial to scanning the princess and drones to see what their primary and secondary allels are to choose better ones for the next generation.
Automation
Forestry is very much a buildcraft addon, and should be treated as such. If you are not using, at least, buildcraft to automate forestry you are doing Forestry wrong. (Although, as I say that, I recall there is a long standing Buildcraft / Forestry interaction (i.e. bug) that means that, if a game is saved AS bees are ejected into a BC pipe, they can get lost, so really, use any mod OTHER than BC to automate Forestry.)
To generate stacks of drones, to clone bees from stacks of drones, you are going to want to automate apairies by sucking bees out, looping the pipe to push them back in again, and then a less preferred route to place any overflow, plus product, in a chest. If you put a queen in here that was bred from a princess and drone with identical allels, the drones produced will automatically go back in and stack up. Once you have a stack of drones, you can put any hive princess in here, and after a few generations, the resulting princess and drones will be clones of the drone stack.
Pristine vs Ignoble
For some reason the mod authors decided that, even if you find a rare hive after much searching, the mod should have a good chance to give you a big "@#$( you". Watch out for ignoble princesses. If bred into queens and places in Alvearies or Apairies, they have a good chance to not produce a princess when they die, effectively terminating their gene line and all the breeding you put into them. They are good for use in Bee Houses, and to sell to villagers.
Discovering Breeds
When you view a bee using the Beealyzer there is a page that shows all of the bees is can be mutated into. This page starts filled with ?s.
You can fill this page in by actually breeding the different mutations, OR you can build the very obscure Escritoire - which is a table that lets you play a minigame that will discover bee mutations. You need a lot of honey comb to play the minigame.
Discovering the mutations is not actually important as NEI or various wiki have details on all the species and mutations that yield them.
A Possible Process
If I was stuck without Gendustry or any machines to help out, and I was compelled by madness to "do bees" I would try approach it this way.
First, I would breed up to cultivated. Then, I would prepare an area with a number of cultivated hives and princesses, that I might automate to get honeycombs out of. but really this population would serve as a template species and would hold all the beneficial traits I discovered.
Then, each time I mutate a new bee species, I would, over generations, try to capture as many of the new species beneficial genes as possible while retaining the species. Once I have stabilized the genome of the new species (the drones stack), then I would introduce drones back into the cultivated stock and re-breed those to capture the improvements.
Conversely, while mutating a new species, I would use the cultivated drones to introduce traits into the new species pool as required.
All very very tedious.