Yes, inbreeding is VERY bad. Even line breeding is bad in the bearded dragon gene pool, which is very limited right now. If there is even a slim chance your beardies might be related you shouldn't breed them.
Also, because they are babies you definately need to keep them seperate. They should not be allowed to breed until they are about 1.5 years old. This is for their own well-being, and the health and fertility of the eggs they produce. The female needs to be full grown and strong before shouldering the burden of carrying babies. For this reason most breeders keep their males and females in seperate enclosures at all times, except during the breeding season. To keep them all in the same enclosure can lead to stress, and sometimes injuries or death. So just keep that in mind.
Good luck. I'm sure some other more experienced folks will come along with more advicefor you, as well. 
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Amanda
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2.0 bearded dragons (Ocho / Domo-kun)

0.1 kingsnake (Rio)
1.0 ferret (Playstation)
1.0 cat (Wally)
0.1 dog (Tima)