To import your waypoints into geoqo, just call it with the -i switch. It auto-recognizes a number of file types (.gpx being the most important).
geoqo -i myfile.gpx
If you have a .zip file from a recent pocket query, don't even bother extracting it first. geoqo can open it and pull out the contents for you:
geoqo -i myfile.zip
Your data will be stored in sets within geoqo. You can refer to that data later based on the set name (which will be based on the pocket query name). If your pocket query was named "somewhere" then you'll have a set of waypoints in your geoqo database named "import:somewhere" automatically for you. See the searching documentation for how to refer to these sets when searching through your database.
Extra feature: comparing against your last pocket query
Finally, if you want to see the difference from the last time you imported a .gpx file the diff "modify" module will compare the results for you:
geoqo -i myfile.gpx+diff:out=myhtmlfile.html
This tells geoqo to import the myfile.gpx file, then run the "diff" module on the results and put the output into "myhtmlfile.html". You can then open the "myhtmlfile.html" in your browser and it'll show you a nicely formatted set of changes between the previous import and you current one.