look up mendelian inheritance.
basically, a 2x2 square.
take the traits from each parent down each side, cross.
this picture takes most of the basics for mendelian genetics, but theres a few key differences between that and bees, as dominance only plays a role in choosing what traits the queen has.
recessive, or inactive traits, only take part when picking the decendents, the choice is random. no dominance in the mendelian sense.
say youre crossing a rocky with a meadows.
all resultants will be hybrids.
15% chance one will have the "common" species trait.
crossing two hybrids:
25% chance of a pure bee
50% chance of hybrid
25% chance of the other pure bee.
if you breed a hybrid with a pure bee,
50% chance of a pure bee of the same type as the starting pure
50% chance for a hybrid.
this assumes there are only two species traits being used.
the fertility trait boosts your odds.
basically, the system rolls the dice 4 times for max fertility, so you will probably see 1-2 pure bees, 2-3 hybrids.
x1 fertility is BAD. youre relying on a SINGLE dice roll to decide everything. basically a very good way to lose a hybrid mutation that you bred with a bee that didnt also have that mutation. (1 of 4 traits is the mutation)
in a practical sense, figure out the next bee in line, grab the two that generate it, breed them together, and thier hybrids together, until the desired trait comes out for both active and inactive on both a princess and a drone.
dont use outside drones unless you dont catch and remove a active 1x fertility trait.
only use whats generated by this apiary.
for converting a princess, you will want several of the drones of the species you want to generate. you want these to stack.
discard whatever drones this produces, use your stacked drones with the princess. this will eventually force out everything else but the traits on those drones.