You should go through the courts to establish custody. They can demand that she take a paternity test and then you can proceed from there. If the kids are his, and HE wants to be the legal guardian then he can file for custody. I doubt the mother is going to give up all her rights which would then allow you to adopt them and be the other parent of his kids.
He can get custody because of her record if she is currently unstable or using drugs, etc... but that does not take her rights away as the mother. You still couldnt adopt them unless she signs off of all of her rights.

