The Application Management document mentions two methods of running a baseline/compliance scan. 1) Run the baseline task on each client computer to generate a baseline for the computer. Then run the compliance scan based upon each computers own baseline. The second option is to create a single baseline and run the compliance scans of all computers against this single scan.
The Application Management 6.1 Reference Guide does not explain the process for doing this.
Run the baseline policy on the baseline computer to create the baseline.bls snapshot file.
Put the snapshot into the FilebaseLine Package on the NS so that it is pushed out to all computers in the specified collection.
Create a new compliance task using the "/baseline filename" and "/o path" command lines to point the compliance scan to the package location on the client and output the data the compliance scan produces to a different location.