You can leave than as is for now unless the male becomes to aggresive with her again trying to breed. I would not move the prego female due to the fact that it could stress her and she may abort or have the pups premature. If you need to you can sperate the breeding male from the group.
As far as when the pups are born I seperate mine right away and put them in a seperate tank from the adults. This is because some adults will kill the pups, bang them around by accident, outcompete the pups for food and it's easier to see what pups are feeding or not. My seperate tank is either run off the same system as the parents or I use the tank water from the parent tank in the pup tank.