
Don't see why you would need to separate during pregnancy and rearing, any more than you do now for safety due to size differences. The bitches should have their pups in a room away from the other dogs until they are two to three weeks old, by then they will not mind the other dogs around.
Pups will be safely in a pen, and no self respecting male will want anything to do with the little piranhas, and Mums will make it clear how much interaction they will allow. Also once outside for fresh air it is best to puppy panel a part of the garden for pups to they are safer (pups can squeeze into the smallest spaces, under/through gates etc), and the adults can get away from them.
Most recently I was in a similar situation as you, except I had a male of 4 years come back 4 days before his sister whelped a litter.
He was restricted to the kitchen along with the others, while his sister had her pups in the living room, with just baby gate between. She had to go out through the rest of the dogs to toilet, so they were all aware of what was going on, though of course they could hear, and probably just about see the whelping box.
My only worries had been whether she would accept the presence of her brother who was a stranger to her, so close to whelping.