My memory is that I had a number of CSV files in a folder, and pointed poiloader at the folder when I ran it.
A single POI file was created that I copied to my Vista HCx.
In use, I do Find --> Custom Points of Interest, and get a mixed list of points close to my location. I can filter the list to a particular category by Menu --> Select Database. The database (category) names were taken from the filenames of the original CSV files, iirc.
The selected database is not remembered between Finds.
The only way of update is to rerun poiloader with amended CSV files, so don't lose your CSV files after you've got your POIs loaded into the GPS.
As far as I know, you can't muck about with the other categories (hotels, attractions, atms etc). They are either preloaded when you buy the GPS, or they come with the map data.