What is the difference between GPX files and Pocket Queries / Queries?
GPX files contain the generic information for waypoints, like the location, the description, the owner, some of the logs, attributes, the trackables etc. The GPS Exchange Format and the Groundspeak name space are pretty much the standard and many other applications and devices use it.
Pocket Queries are defined by Groundspeak and contain additional information in it like favourite points, found date and images. If you have access to the Groundspeak Live API, use Pocket Queries as they give more information. The "Refresh Waypoint" in the waypoint, the "Load Waypoints" in the map and the Query page retrieve the data in the Pocket Query format. If you don't have access to the Groundspeak Live API, use the GPX files.
Queries are defined by Geocaching Australia and, like Pocket Queries, contain additional information in it like ratings and type. The "Refresh Waypoint" in the waypoint and the "Load Waypoints" in the map return the GCA Queries. The Query page for GCA uses GPX.