Cant add rivers and lakes after sculpting

Sculpting a game level, and am sculpting the underwater ocean section. Problem one is you have to add the ocean first which has its own seperate layer. I then need to create a layer above it to sculpt the level for under the ocean. Everything works fine up to this point. But as I add another layer to start sculpting the sections out of the ocean, I cant add rivers etc… to newly sculpted areas. The reason for this is any water I add gets added to that original water layer so its only reading whats below it obviously. I need a way to add water layers above the current layer ive sculpted. So it deforms the new sculpted terrain not the old sculpted terrain. Has anyone figured a way around this? I cant for the life of me get the custom waterbody to work. I would love it if the rivers and lakes didnt deform the landscape, it has a check box for it, but doesnt work.