My two boys, Clyde and Scooter have lived together for almost 3 years, and they STILL fight. Of course it is much less often, and they usually will just give each other a quick slap and move on. They are never going to be friends, but they have learned to tolerated each other for the most part, and will avoid each other most of the time. I lived in a 1 bedroom apartment with each other, and they just got used to being in different rooms.
Last night the boys did have a rather heated "arguement" that ended with Scooter scratching Clyde on the nose, and Clyde spiking Scooter (and losing a claw in the process). Today they are giving each other a wide bearth.
It does take time, but the cats will work things out where they will either like each other or tolerate each other.