My cats

My 2 cats who grew up together as kittens are fighting with one another now as adults , they are girl and boy as well. The male cat had to live somewhere else and after my mom died, the owner of the male cat who is my dads friend has agreed to live with me and my dad, so the male cat had to go back home.

They seem ok and can be in the same room as each other. But they have woken me with their fighting when they bump into each other and sometimes one of them will just pick on the other cat.

The female cat is a petite cat and she has had broken legs because of the male sometimes. I am concerned about the female cat and that she will get hurt again or worse. My mom before she died told me to look after her as well, I don't want to lose one of the cats!

Have both the animals been spayed / neutered?
This will help bring their aggression levels down.

If they were separated for some time, it's likely one has established its territory in your house. Cats are often very territorial animals meaning they will fight to maintain that dominance. Considering you've said the male has broken the female's legs before, this can get extremely violent. The cats should be kept in separate rooms with the doors closed. They can sniff each other through the crack under the doors but leave it at that. Let them sniff each others' blankets and bedding material to let them get accustomed to their scents.

Also have at least 3 separate litter boxes. One for each cat + 1

They have been spayed and neutered when they were younger. The female has always been living here so I think it's the female but I caught the male cat pouncing on the female last night. The cats go outside but the male also uses a litter box, I don't think the female uses it