If you purchase birds from a breeder, they generally have vastly smaller flocks than do hatcheries, so depending on the breeder, you may want to get birds from two different lines (two different breeders) to begin with... or not, if you don't see any breeding problems. Keep in mind that "line breeding"--breeding a rooster or hen to its own offspring--is actually one of the most important ways breeders improve their birds. They breed an outstanding example of a bird into their flock, and then every so often bring in a new "line" to make certain there is enough genetic diversity. Hatchery stock from major hatcheries is so diverse, seeking out new lines will not likely be an issue for you for several years. This is especially true with very common breeds like Orpingtons, Rhode Island Reds, Wyandottes and so forth. This is because they're popular to keep, so the breeding flocks have to be especially large to keep up with demand.
No matter where you choose to get your birds, after several generations of having a "closed" flock at your home, you will probably want to introduce new genetic material via a new rooster at the least, and possibly some hens as well. It may take a few generations to even be able to identify flaws you want to address.