As for the Imprinter, how it works is the two species on the left are how you choose your resulting bee's both Primary and Secondary species. If you want a single species (i.e. Diligent Princess) you would select that species twice (i.e. Diligent / Diligent ) and then drop any princess bee in the imprinter's upper right slot.
For hybrids, you pick the dominant gene first, then the recessive gene. So for a say, Diligent-Cultivated Hybrid Drone, you would pick Diligent up top, Cultivated on the bottom, and drop in whatever drone you want to transmogrify.
Hope that's easy enough to follow. :3