i did save map file in external sd card, basically you can put it where you want, but you must edit ~/.navit/navit.xml (or /usr/share/navit/navit.xml, but i think it would be rewritten at every installation) to point to that file.
you could give a look at these two useful pages of navit's wiki:
http://wiki.navit-project.org/index....figuring_Navit
http://wiki.navit-project.org/index....n770/n800/n810
you will save a lot of time