OK, well I am not an expert on pregnancy and newborns but I can give you a bit of advice while we wait for more experienced members to come along. Basically, the first thing that you nee to be aware of is that this is a pro-rescue, anti-breeding forum due to the number of unwanted guinea pigs that are in rescues. So while we are happy to help with any other advice there isn't a single member on this forum that will give you advice on putting the male back with the females.
Chances are that your other female is pregnant as well so I would be watching out for more babies popping along.
Best end results is that you keep all the females together in one cage (if the current cage is big enough) and that one of the babies is a male and you can house him in a different cage with your other male.
As I said - I am no expert on pregnancy and care of newborns but you will find some useful info on this forum but there will be other experienced members coming along later on today who will be able to give you tons more info.
Personally - I would love to see some photos of your piggies when you get a chance.