The only reason to separate the males from the females is if you don't want the females getting pregnant right after birth. A female can get pregnant within 24 hours of giving birth, and there are some people who prefer to give the mom a small break between litters. Some don't, it is all a matter of preference.

In my experience, males help take care of the babies. I have seen my big boy sitting on a litter while the mom is eating. While I have also had others that could care less about the babies and leave them alone. I have never had a male who was in with his own offspring, kill them. Now, if the offspring are not those of the male's, he might kill them in order to ensure his own genetic success, but other than that, you should be fine.