This how to assumes that you have already opened gpx or kml file in GPX Viewer. If you haven't opened it yet here is How to open gpx or kml file. Please note that icons for waypoints are not saved, but cached, so if you clean Opened files cache in Clear cache data in Miscellaneous Settings these settings for icons for waypoints will be deleted.

Below are step-by-step instructions on how to change an icon for a waypoint.

1. Tap on waypoint icon on the map.
2. After tapping on the waypoint icon tap on bubble text shown above the waypoint icon (if the waypoint does not have any name or description, go to the left main menu, then select the Waypoint info option, and find your waypoint by listing it with < and > button in the top bar).
3. Scroll a little bit down and tap on the “…” button.
4. From menu select Set waypoint icon option.
5. From shown dialog select Choose icon from library.
6. Choose some icon you like from the library and tap on it.
7. Go back to the map screen and see your icon changed.

Below is a video showing the instructions above: