The thing to keep in mind in any breeding program is that you are, in
general, not *creating* anything new -- such creation of "new" is due to
largely random mutation and/or recombination of existing genes.

What you are instead doing, is a process of elimination -- removing genetic
combinations that you don't like from the breeding population.
With honey bees, due to their sex determination gene, the problem is to
remove what you don't like, while at the same time conserving an adequate
diversity of sex alleles in that population.

As Trish points out, unless you've got a LOT of colonies in your managed
population, relative to the TOTAL number of colonies (yours, other managed,
or feral) within flight range of your mating, there will be some degree of
outmating with drones not in your breeding program.  For a small,
non-isolated breeding program, this will likely help to prevent an
unacceptable loss of sex alleles, but will at the same time make it more
difficult to bottleneck the genetics of your breeding population.

Thus, it may be most effective to practice "negative selection" --
eliminating colonies with traits that you really don't like.
This would be opposed to "positive selection" -- in which you choose the
few breeders exhibiting a trait or trait that you strongly want to select
for.

In my own breeding program, I do both.  With regard to mite resistance, I
positively select for queens that headed colonies that prevented varroa
increase, and negatively select against (by killing those queens as soon as
we identify them) colonies in which varroa was able to explode.

-- 
Randy Oliver
Grass Valley, CA
www.ScientificBeekeeping.com

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