I think just keeping him on the upper level of the cage will be fine until you've sorted things out. When the babies are 6-8 weeks old (they can be separated from mom at 6 weeks, and are usually easily introduced to an adult before 8 weeks), determine who are males and put them in with their father after an intro on neutral territory.
When I found out that one of my four 'females' was male and that all three of the actual females were pregnant, I had to separate him from the others. He spent a couple of months on his own in a smaller cage; it being next to the others' cage I think helped. However, he was so, so happy when he was finally moved into a large four-level cage and then have his four sons join him.