cyanogenmod recovery

Hello guys,
i don't really have a problem with my Atrix, i was just wondering why i should update the recovery even if i just install zip files and so on.... well actually i don't understand how it works, i mena, does it run in background even after the S is booted? Plus, is a problem to update the clockwork with the cyanogenmod recovery downloaded from the cyanogenmod website? which are the pros doing it? Thanls in advance and sorry for my (maybe) stupid question :v