No doubt you can use POILoader for saving and using your favorite database. You must create separate folder with unique name for each of your categories.
But you can try to edit categories in Mapsource too. In settings create your categories by name and then you can pick up its in waypoint properties. You can also mark several favourites with shift or control key and then change waypoint properties for this group. I do it for competitions and adventure when I would need to load waypoint in Nuvies under events category.
P.S. temp.gpx (or others) is more suitable than current.gpx. In this case the uploaded gpx files stay in device as original and would be restored after reset. If you want replace favourite just clear all in device menu and after replace saved gpx file.
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