Backing up your settings in Maemo's standard backup tool will suffice. Maemo Mapper keeps its configuration in gconf, which is backed up with the rest of Maemo's settings.

The only data that isn't backed up via the standard backup tool are maps, POI, and the current track/route. The first two can be easily stored (and referenced) in a memory card. The current track/route are stored in a file located at /home/user/.maemo-mapper/paths.db. If you want to keep the current track/route, you need to copy that file onto a memory card, and copy it back to the same location (/home/user/.maemo-mapper/paths.db) after you've reflashed.