Well, after working on basins all day long, I think I found a good method for working on them. The problem has been finding the actual low point of the edge of the basin, so that lowering the altitude there actually affects things. Filling basins with land was not easy to spot those areas. Filling with water is better, and also easier to work with, since you can erase land while the water is still there and still reset the water later back to sea level.