With Extra Bees, there is also something very important you need to know:
The Apiarist's Database is your Very Best Friend, right after the Beealyzer. (Also, look up Frames - they'll boost your honey production so you'll have plenty for beenalysis.)
Seriously, the thing is worth the emerald you need to make it many, many times over, just for consolidating all the biome and evolutionary data you'll get.
It also has an advantage over the beenalyzer: you'll be able to see the colors (if not the names) of "Further Mutation" bees, so if two of your bees can be crossbred, you'll know. See below.
Although there's an odd bug/feature right now where all bees in the evolutionary tables are listed as "Discovered Species" until you actually achieve the mutation. Eh.
Also, squeezing honey drops/honeydew into liquid honey has a small chance of getting you propolis. Mind you, you'll later breed a bee which is far better at getting you the gooey stuff, but if you want some for rubber right now, there you go.
One more thing: the Alveary can't adjust humidity, and certain bees will produce very valuable 'specialties' (most notably, two ingredients for Alvearies), but only in their 'preferred biome' - that is, even if you manage to breed bees that will tolerate anything, they won't produce that special stuff unless they're in their favourite conditions, so plan accordingly. Luckily, there are only three possible humidities - so if you manage to find a place where all three meet, feel free to celebrate.
(If you feel like looking for hints, you could go to the Forestry website. I believe under the bee breeding section, there are a table of hints for how to get some of the more interesting families, including the biome-locked ones. Of course the Database will also list the mutations, but I'm not sure whether it'll list which ones are biome specific. Certainly not before you actually get them)
PS. Blue means recessive, so getting 3x or 4x fertility is usually not worth the effort, except for some very special tricks.
Edit: I found out just now that the mutations database has been 'fixed' in a newer version of ExtraBees - so the current version can be considered a bug. Whoops! It seems I discovered how to make one very overpowered bee through exploits, then... oh well.