Help with dimension generation

So I've noticed that for some reason, no matter what I do, the caves will be full of water. I've also noticed that, while not a problem currently but could be a problem in the future (since the mod I'm making has multiple dimensions and currently the one I'm working on is meant to be a dark form of the Overworld), no matter what settings I put for the biomes, they're exactly the same to the Overworld. For example, even though there's no mountain biome set for the dimension I had made, there's still mountains in the same spot as in the overworld. How would I change the generation so it's different from the overworld but similar (similar in terms of generation but won't have mountains in the same spot as the overworld, caves are in different spots and are different shapes, ect. Similar to if you made a new seed)