Hmmm. Just as a quick start, notwithstanding traits. Things like "shortest life" and "fastest worker" go a long way in helping you breed more drones for breeding/DNA and producing more comb per cycle (thus more product).
When you put a drone and princess pair into the apiary/alveary, there are two realms of possibility.
1. If they are a non-mutating pair (i.e. there are no possible mutations from that pair breeding) then you have a chance of producing a princess of either type, along with however many drones they produce as effected by their fertility which can range from x1 - x4 (I think).
2. If they are a mutating pair, you have the chance of (1) occuring, or that one of the offspring, whether it be princess or drone, to be born as a mutation. For example, breeding a meadows bee and a forest bee together has a chance of mutating into a common bee. This is how you progress.
But given (1), it is possible, once you have the mutated species (and producing pure bred offspring), to skip (2). Simply by breeding any non-mutating bee with your already acquired species (through PREVIOUS mutation), you can try and straight convert that bee into the one you want.
It is subtle, but that is the progression in bees. Low chances of mutation, thus difficulty in acquiring a breeding pair, is what holds you back, and what most of your strategy should be formed around. Once you have achieved a mutation and stabilized that pair (producing pure bred), then you can simply go for path (1) in creating more instance of that species you like. This leads into higher tier mutations that require previous mutations, going back to having multiple breeding pairs, as to achieve a higher probability of success.