Segregation doesn't have to be a bad thing. It just means that the cats can have some peace and quiet away from the dog. I have a second bedroom that only my cat can access. What I've done is place a heavy old card table in the doorway, and it's wedged in the doorframe with a huge cat tree in the hallway. So my cat has no trouble getting in and out of the room but the dogs are blocked from entering it.
If you make a plan now on how to house them, it should be fairly easy. Just take it slow, and don't expect too much from them at first. Just keep them safe - you don't want the cats getting cornered and scratching the dog either.