Get your rats from another source. Most breeders who take it seriously will selectively breed out the bully males. Raise them from babies together like you said. They are naturally clean animals, you just need to give them options. Give them a place to sleep that's off the ground and give multiple litter boxes for them to go in on the ground. Put a few drops of vanilla extract in their water to cut down on scent and above all - feed a good diet to avoid bad smell and frequent bathroom needs. When you clean, keep soiled bedding in the litter boxes to help them understand they should go in the smelly place.

X3 about the allergies - if you're allergic, you're allergic.