I've found that identifying mistakes and choosing punch-points for the drums in the studio tends to waste time.
I would say set up 3 different playlists for your drums and simply record a minimum of 3 different takes per song (depending how good the drummer is.. if he's shit you may want more just in case). That way his rhythm isn't broken up, as he simply plays through the song the whole way 3 times, and you don't have to use as much time/brainpower identifying what is wrong. Sometimes in the studio you get so 'in the zone' you wouldn't hear a mistake if it jumped out of the session and kicked you out of that director's chair.
After the drums are all recorded. Take that crap home and edit it up with an mbox and some cans.
EDIT: Shit, just realized you were using Cubase. Well, I've found Cubase to suck at tracking, but you can still pull out 3 whole different takes of the drums and just have them all overlap. You can right click then choose which you want to bring 'to front'. Good luck editing them together though... probably take you 10 times as long as it would on PT.