If the male was in the cage when the pups were born, the female is almost certainly pregnant again -- she can become pregnant within minutes of giving birth. And that's VERY hard on the sow and on the second litter of pups. Make sure she gets very high quality pellets and hay, good veggies, and supplemental vitamin C.
Separate him now, and keep him separated. There's no need to put the cages next to each other, but if you do, put a lid on the FEMALE cage. A determined male can push up the lid on his own cage to get to a female, but he can't lift the lid on the female's cage.
If one or both of the pups are male, they can go live with their dad when they're 21 days old. That's when the boy pups have to be separated from their mom and sisters to keep from having inbred litters.
Please don't allow your pigs to breed. Pregnancy and labor are very hard on guinea pig sows and pups, and the death rate is high. Guinea pigs are also susceptible to a number of awful genetic conditions, at least one of which (lethal white syndrome) causes the pups to be born blind and deaf, with wonky and/or missing teeth and immature digestive tracts. They need lifelong, expensive vet care. Another condition, osteodystrophy, causes a painful, untreatable bone and joint disease.
