I can tell you exactly how to do bees according to Binnie (I've never touched the Gendustry mod, I only do my bees manually and using Binnie's mods (i.e. Genetics).
However, I don't visit this forum very often anymore because I don't play Minecraft very often anymore because I don't find the game to be as exciting as it used to be. After you've played 10 modpacks with mostly the same mods, after you've done a mod like Thaumcraft a bunch of times... it just doesn't seem as interesting. I wish I could go back in time to FTB Ultimate days when everything in the game was so new and awesome. sigh
Anyhow, I'll try to make this brief. When you do your mutations to make a new species, the key idea is that you want to be mutating as FEW genes as possible - basically, you want to cross breed two bees having identical traits EXCEPT for their species. So what I always do is make what I call my "Super Bee". I use Cultivated bees for my super bees, simply because you get them early, and because they already have the "Fastest Production" gene by default. So that's one gene you don't have to worry about adding to your Super Bees. Essentially, just find the best traits you can and apply them to your Super Bee princess and drone. Every time you find a better trait than one you had, put it onto your super bee. When you're ready to make a new species, take a Super Bee princess and put one species on it. Then apply the other species to your drone. Now breed the two together - since both princess and drone are identical except for species and all other genes match perfectly, there's nothing that can happen to mess up the entire operation. Use an Alveary with a few mutation blocks (I use Eye of Ender in them) and you can bang out new species after new species very quickly by hand. Just keep building your "library" of all the different species in Serum Vials until you've made all the useful bees.
Hope that helps! Bees is a long slow process indeed, but for me it is always a labor of love. I hate doing Thaumcraft all over again for the umpteenth time but I LOVE doing bees, it never gets old.