Cats pees everywhere and antagonizes my female cat. HELP?

Do what you have to do girl. I have had this problem with no resolution so I made them outdoor/indoor kitties now. My fiance and I had a room about 10x10 in the back of our house. It has a door with a viewing window from inside the house and also access to outside as well. We call it "The kitty coop!" It seems to work out for them, but I also live in the country and don't have to worry about cars. So, if I were you... don't put him in a cage, but maybe in the bathroom. That way if he decides to pee everywhere... at least you can clean it up. Put a litter box, food, water, a soft place to sleep, and maybe a toy or two for him. As, for your other kitty, poor old girl.