If you're using it to save configurations, you'll need to look at the Archive status to make sure the configs are getting backed up on a regular basis. Startup/Running out of sync reports are good to make sure writes were done when the configs were modified. Custom reports can be useful when trying to produce inventory reports. If you're using it for sylog management, it's a good idea to look at the syslog reports on a daily basis. Custom syslog reports can be created here to keep you from having to look through a lot of different reports to find potential problems. Campus manager produces descrepancy reports but I've never found them very useful.
I'm not sure which version you're running but I know with lms 2.2 I'm always faced with problems in trying to get data out into a nice presentable format.
I can tell you're new to CiscoWorks because you said it's been great so far....give it some time!
