Prism Patch Manager already has the "auto query" feature.  Please click on File-->Agent-->Settings-->General Tab.  Under the "Back Ground Query" section, you can schedule your queries to take place after hours.  I would recommend doing this 1 day a week and scheduling it after hours.

In regards to the queries, PPM will query as many machines as your machine will allow.  It bases it queries on your processor/memory and your bandwidth.  Another thing to try would be stopping & starting your UEAgent service before you query your machines.  Doing that will always improve your performance.

If you have any other questions, please let us know.

Thank You!