On larger boats, the cockpit covers usually starts from just under the bridge deck and slopes back to the transom. It usually has sides, making it fully enclosed, although some have no sides, just a sloping back piece. There is usually a zipper access to the bridge and maybe access astern.
A second type of cockpit cover is usually for smaller boats. It generally starts at the bottom of the windshield, goes up to the top of the windshield, and then aft to the transom.
Cockpit covers are generally just used for the protection of the boat, and are not used when underway.