Some very experienced breeders do line breeding. It is not suggested, though, because a puppy can carry an undesirable gene (such as the gene that makes a puppy more susceptible to cancer, or the gene that causes compromised immunity) but he may not "show" this problem. He may be a carrier, but the gene is not "dominate". However, when you get two of these dogs together the gene then can become dominate in their off-spring. They have "half" a gene (so to speak) from Mom and "half" a gene from Dad, now it is a "whole" gene and the problem shows out.
Your dogs may or may not have these genes. Only some can be detected by testing. Some breeders do extensive testing such as for eye problems and you can read about those tests online. This does help reduce the "passing on" of problems because if a dog has these genes, the breeders do not use them for breeding.
Since your dogs have already mated, don't fret over it. Do a bunch of reading about whelping and get yourself prepared. Be ready for an easy delivery, and be ready for a very rough one. That way you are ready for anything.
The above link provides some information on the pregnancy timeline and things you should do for your female. Don't dwell on the "before mating" information right now, because what is done is done. It is a lot of work to whelp puppies, but you can do it. Just find out all the information you can and definitely call your vet today and see when he wants to examine your female. Make all the appointments he asks for, and keep those babies in good health. Then comes the time for adopting them out. I believe the above link also has suggestions for finding good, responsible homes for your babies.
Some people may try to make you feel bad, but you just have to keep your head up...it happens. If the whelping was too much for you this time, then do see about getting your pets spayed/neutered. If you enjoyed it, look into the suggestions from good breeders and become one yourself!