I saw a post where a user was allowed to actively log in and run PerfMon. Is there a way to set it up where I can create a dummy user, tell the Counter Log to run as the user, and tell it to go? Or does someone actively have to be logged in and running PerfMon?
It depends on what your trying to achieve.
If you want an interactive logon from a non-privileged user, then you just have to allow the user to log in, either by adding them to the remote desktop users group, or by updating the local security policy and granting that user the log on locally privilege.
Alternatively, if you are just trying to capture perfmon stats, then simply log in as an administrative user to the server, set up the counter log, start it collecting, and log off the machine. It will continue to collect in the background.
You can use the runas command in a script to accomplish this if you really want to. The arguments for the command are here.
Try a remote interactive session:
http://wiki.imacros.net/How_to_Schedule_a_RemoteInteractive_Session