I breed my bees manually, although I do use the acclimitizer from time to time to rescue a bad mating where the resultant bee won't work in an environment I have available.
As soon as you are able, set up automated apiaries to continually produce drones. Create an apiary for each pure mating set you have available. You will need lots and lots of drones for breeding bees manually. The rest can be recycled or turned into liquid DNA for the extra bee machines. For automated apiary setups check this thread on page 3 and following.
http://forum.feed-the-beast.com/threads/beekeeping-guide-yay-or-nay.7173/page-3
First step is 4x fertility. I normally use a marble princess as the base mating pair along with a wintery drone. The only 2 traits that are important are the marble species and the 4x fertility. I use the marble princess as I don't have to be in a snow biome to mate them. The first generation is normally a 50/50 hybrid of the two. If you are lucky, you can breed the resultant bees in a normal biome, if not, you will need to use the acclimitizer, or find a snowy biome for the next mating. After the second mating, I look for any bees that have the 4x fertility. Preferably in more than one spot. Also look for the marble species train in as many spots as possible. I also try and get rid of the freezing effect, but not at the risk of 4x fertility or species. The rest of the traits don't matter at this point in time and can be ignored. These will be bred in by other bees later.
Keep breeding the bees together until you end up with a marble princess with 4x fertility in both spots. Once you have this, put the bees in an automated apiary to start producing drones. You will need lots and lots of drones for breeding the other bee lines.
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As far as your original question, keep any bees that have the forest trait and 4x fertility. nothing else matters. Breed the bees together. Having 2x/4x fertility on the drones is fine. It is the princess that determines the number of drones produced by the mating, so having the 3x/4x on the princess is awesome at this step.
It will probably take several generations to get 4x fertility and forest on both your drones and princess to finally have a stabilized genetic pattern. (where every mating results in identical offspring)
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Back to the guide -
I keep one genetically pure pair of bees in the automated apiaries until I have a stack of 64 drones, or until I clone the genetic line into another princess and drone.
To clone a princess, you take a dozen or so drones, and rebreed the princess with those drones until the princess and the drones have the same genetic makeup. You discard any new drones produced along the way.
Once you have a clone (or multiple) of the princess and an identical breeding drone, the next step is to go for common and/or cultivated. Breed one of your 4x fertility princesses along with the highest fertility hive bee of another species. It's ok if it is 2x fertility. It doesn't matter at this point. If you are going to be around the apiary, put in chocolate frames to start, then swap them out with soul frames to encourage mutations. If you are doing other things, just put in the soul frames and check on them later.
If you end up with a common drone, just set it aside for the moment. What you are really wanting is a common species on the princess. Sometimes in this phase I will end up with cultivated-common princess. If you end up with cultivated, that's ok too. Once you have one of the cultivated or common species, it is a lot easier to get the other later. Once you get common on the princess, breed it together with the common drone. If you were breeding together forest and marble species to get your common, try breeding together a common-forest princess with a common-marble drone. This will give you a 50% chance for common, and only 25% chance for marble or forest. Since they are opposite hive bees that can mutate into common, use soul frames for the additional chance to get a mutation. (This will sometimes give you a cultivated bee as well, but that is ok.) Once you have a common or cultivated bee, start trying to purify the line to either common or cultivated. If you get to cultivated, try and keep the fast worker trait. Try to keep the 4x fertility along the way as well, but don't worry if you lose it. You can breed it back in once you have the species stabilized.
After stabilizing the species, clone the princess again. You now have the original line for producing more drones, and this guarantees that you never lose a bee line as you are trying to mutate them or bring in other traits to the line.
Now that you have your common (or cultivated) line, breed it back with your original 4x fertility line. Now you are going for the 4x fertility and the common species. The rest of the traits don't matter as common does not have any special traits that are worth keeping. I recommend chocolate frames or if you are on 1.5.1, use the new bee house in forestry. You can't use any frames, but you also have a 0% chance for mutations. perfect for breeding in traits and purifying the bee line.
Once you have a 4x common and a 4x hive bee, breed those together and go for a 4x cultivated line. Each time a bee mutates, the genetics will be the base for that bee, so you will have to breed in the 4x fertility again, but it you are lucky, you will end up with it on the half of the bee that didn't mutate, so it makes it much easier to breed back in.
How to breed in the bees with 1x fertility - Use a 4x princess and breed it in with a 1x drone. You will then have at least 1 generation to with 4x fertility. Keep all the drones from this breeding. Now since your princess will likely have a 1x fertility as well, repurify the princess so it has 4x fertility again. If you are going for rocky bees, use a cultivated princess (or a bee house) as the cultivated line does not mutate with the rocky. Now, breed your 4x fertility princess with one of the drones from the previous mating. Since those drones will have both 1x fertility and 4x fertility, you have at least a 75% chance to end up with 4x fertility in the new generation. Try to keep as many of the traits you are able, but go for 4x fertility and species first and foremost. Once you have stabilized the line with 4x fertility and as many of the traits as possible, clone this line again (see a pattern?), and breed the princess (with 4x fertility) with one of the original breeding drones from the very first mating. This time, you are looking for any traits that were lost the first time around. Try and keep 4x fertility and the new traits. Go for traits above fertility this time as you already have a stabilized line with 4x that you can breed back in if necessary.
Each time you try and breed in traits, pick one trait, and try and breed that in. Since you clone your line each and every time, you never lose your current progress. It does add in a few extra steps, but also prevents the total collapse as you experienced earlier when you ended up with tropical bees.
Each time I mutate a species, I go for any traits and species that are specific to that bee line that I don't already have elsewhere. Then I go for fertility. Once you have a stabilized line, you can bring over the traits you want into your other bees. The apiarist databank is a good source of information for this as it shows the base traits of the species.