I just leave the males in all the time. Rats and mice. If you do separate, do like Brendan, and pull female out before she has babies. Then when you reintroduce them, put the female back in the males cage, not the other way around. That will cut down on the aggression, as males aren't territorial about females, like the females are with a male.
Never had any trouble with the male rats chomping on the pups. Just don't add a male to a cage with nursing pups, even if they are his own. Either keep them together from the start, or wait till they are weaned. Rats aren't so bad about this as mice, but better safe than sorry.
About as far as helping the male will go is sleeping on the pups, but I don't think it's to keep the babies warm as much as himself. Male mice tend to be more helpful with their babies.