Secondly, whether you should roll once for each creature or one for all creatures depends entirely upon expedience. Sometimes it's best to just roll the once and then have that number checked against all of the creatures present (keeping in mind that you're rolling against their Stealth); sometimes it's better to roll for each creature independently (if you do this, make sure you either make the rolls secretly or do something else to obfuscate the number of enemies that you rolled for; some GMs will actually "pre-roll" a sheet of numbers and scratch them off as they go in order to prevent players from hearing them roll).
Whether a door is total cover largely depends upon the door. Keep in mind that arrow slits (which are 3-4" wide) provide superior cover. Of course, it's also important to note that arrow slits are designed to provide access to a person at usable heights while doors don't really do this (so an attack underneath a door will hit feet while an attack through an arrow slit will hit more vital portions of a target).Anyway, this also begs the question, if doors are not ruled as total cover for the purpose of spells
I would tackle whether doors are total, superior, or normal cover on a case-by-case basis (tell your players before they start rolling though so they know what you've decided before they've committed and can't take it back).