Check this site, it explains inbreeding and linebreeding. http://bowlingsite.mcf.com/Genetics/Inbreeding.html
I think that you should sex them and separate them too. Inbreeding is actually a powerful breeding tool when you want to isolate a recessive gene. But, should only be attempted when you know the genetic background of the animals, still you risk having some problems, as inbreeding is done to get homozigous animals (having 2 copies of the same gene; XX or xx), that's why it's helpful to get out a recessive gene... again this is exactly the problem, as most, if not all, genetic diseases are recessive, so you can bring them to show up by doing inbreeding. You can have generetions of carriers and never get the disease to show up, and then have a disease show up once you do inbreeding, cause the recessive gene that causes it can be carried hidden. You can easily get rid of a dominant gene in your population of animals, but it's impossible to get rid of a recessive gene.
A person I know online that breeds gerbils had something happen that might help me explain what I'm trying to say:
She has a clan of gerbils, all with known genetics and can consistenly predict the babies of her breeding pairs. She had an oops litter of one her pairs. She had left a daughter in with mom and dad cause she was a runt, and was really behind. Well, dad mated with daughter and she had a surprise litter. Both were golden agouti, and with the genotype they had, the pups where supposed to be all golden agouti. Well, one pup wasn't, it was dark eyed honey. Well, redoing all genetics, she found out that dad must have a hidden recessive (Ee), and daughter inherited the recessive e from dad, and when they mated, they had a baby that was ee. This same thing can happen with any gene.