This may border on off-topic for what you want, but there's been several large threads on this forum about how rats really shouldn't ever be housed by themselves - unless you have an individual that just won't tolerate rat company. Even if you're "only" breeding feeders or something, it's still more humane to the rat if you can get one that's already bonded to a buddy (to cut down the risk of fighting if you just throw two strange males together). They are very intelligent animals and do get lonely.
So should I just get 2 pairs of rats per cage? What happens when the babies are born and what not? I don't know how rats act compared to hamsters, but I had a pair of hamsters, and the male would frequently eat some of the babies.This may border on off-topic for what you want, but there's been several large threads on this forum about how rats really shouldn't ever be housed by themselves - unless you have an individual that just won't tolerate rat company. Even if you're "only" breeding feeders or something, it's still more humane to the rat if you can get one that's already bonded to a buddy (to cut down the risk of fighting if you just throw two strange males together). They are very intelligent animals and do get lonely.
One pair of rats should be fine, though if you have some REALLY big cages and you make sure everybody gets along you could probably have a large social group of males in one and females in the other. But at minimum probably two rats per cage.
I wouldn't leave the males in, no, just to be safe. Though I haven't done any rat breeding myself, so I could be wrong.
I'm not about to judge feeder rats (I have a python myself, though I mail-order his food in bulk), but I do think that raising one's own feeder rats is going to be problematic. It's going to take a lot of money and time to care for all these, and the odds of having a rat in the right size every single week/two weeks will be low unless you're breeding so many that you'd spending a small fortune on it.
I used to breed/raise rats when I was younger, they are very social animals, and 2 per cage is best. They do need some pretty big cages to be happy, and while it is possible to keep the male and females together (the males help raise the litter) it is a risk because the females go into heat shortly after birth and you could overbreed your female (which stresses them, makes them sick, and can be a cause of cannibalism). If you only want one male for breeding, what about getting another neutered male for company? The smell of the females can cause dominance fighting and result in nasty injuries or death of two intact males. Rats typically don't cannibalize though unless in too-small spaces, stress, or not enough to eat to name a few.
