First and foremost, verify that the "All Applications" metering policy is NOT enabled (Application Metering..Policies..Application Monitors in the 6.5 Console). If it is, your database will grow exponentially and performance will suffer as a result.
It's best to create a new policy for each application you want to track and enable the "send application start events" and "send application stop events" check boxes. The canned reports should be able to get you the data you need.
Chapter 3 of the
Application Metering Solution 6.1 SP2 User's Guide will help explain in more detail. In version 7, Application Metering was rolled into Inventory Solution instead of being a separate solution.