I would keep it on auto-update, but one thing to note that has bothered me in the past, this is probably obvious to some, but when it updates you need to reauthorize your apps for root -- so if you use a scheduled backup like with titanium backup, you need to reopen titanium backup and authorize the root after super su updates because it doesnt remember after the new binary is installed. if you don't do this, titanium backup will complain it cant get root when it tries to run the scheduled backup.