Try doing inner layer of pants, then inner tunnel of top, then outer pants, then skirt tunnel, then outer top. My pants don't have an inner liner so i just do inner tunnel of my dry top, then pants, then outer layer of dry top for rafting and have stayed fairly dry when swimming (relative). Im not sure what else you could do to make it more water proof.
The less complicated and flatter you can get your layers, the better. Hope this helps.
If you are lucky enough to be in the mountains, you are lucky enough.