OK, first of all, a PQ is one of the benefits of becoming a premium member at groundspeak.com
Basically, it will give you a file of geocaches based on criteria you select during its creation.
Yes, it is in .gpx format, which is the perfect format for importing it into GSAK.
Now, GSAK is a database program with an extensive set of user-selectable filters.
If, for example, you create a PQ to return all caches within 50 miles of your home coords that you haven't found, you would load the results of that PQ into GSAK. (keeping the data fresh is another story, but there are several strategies to deal with stale data) Now, assume you want to go caching, but its very hot and you're only going north. You would then filter your GSAK database to show only those caches to the north and maybe only those with a terrain rating of 2 or less. This "filtered" database is what you'd want to upload to your GPS.
Now, for the PN40, I'm not very familiar with it, but I did find a link to a GSAK macro at GSAK.net that might help you upload your GSAK filter to it.
Read this for info.
Again, I can help with GSAK, but as for use with products other than the Garmin models I have, I'd be mostly guessing.