Waterproof Duvet Covers provide extra protection for bed covers.
The zip runs down the side of the cover - making it easy to get the "inner" in and out. The zip part of the cover is not waterproof. On most beds this is the part that hangs over the side of the bed.
If you find that with 3 layers (inner, waterproof liner and outer pattern cover) they all get rucked up inside. You can just pin the corners of the inner and the waterproof liner together. Then it is easier to get in and out of the outer patterned cover.