I am wondering whether or not people do anything specific to minimize the genetic input of mediocre stock in their breeding program.

You breed from the best stock; grafting and creating drone colonies, but don't the middle-of-the-road colonies contribute to the pool through drone production?

Do you maintain breeding yards that only have the finest stock, and isolate them? What if you can't isolate? Would you then make an effort to minimize drone production in hives that you weren't really excited about? Or are the focused efforts of "breeding from the best" enough to simply outweigh the contributions of the lesser stock?