Breeding principles

As a hobbyist who's interested in doing some small-scale breeding, I'm wondering what the general consensus is with "backyard breeding." Horses are what I'm familiar with, and certain breeds are forbidden to outcross with other breeds. A lot of "backyard breeders" do this anyway, and the result is an unregisterable animal, and purists freak out about the integrity of the breed.

With all these new color morphs and fancy lines, is it better for the future of the Leopard Gecko genetics to breed like to like in terms of developed lines - or is it okay and acceptable to buy lizards here and there in terms of what catches the breeders' eye, and just start producing? I mean, I realize that there has to be experimentation and breeding to develop new lines - but as a small home breeder with no aspirations like that - would it be better for me to breed geckos from established and documented lines, and stay within those lines, rather than breeding lizards of unknown ancestry and throwing more mud (should I ever sucessfully sell anybody down the line) into the gene pool?

Is there value (in terms of breeding) to the lineage of the geckos, or is it all phenotype and if the breeding continues, the genotype will establish itself?