The easiest thing to is to install the software in main memory (or persistent storage) and put different maps on different cards. The maps themselves will take up the most space once you have a bunch of them.   

A note from Microsoft says that the .Net files take up space in main memory whether you install them there or not. Pocket PC 2003 already has .Net 1.0, so installing it just updates some files.

The program itself can be installed to a card, but the Start Menu shortcut may not find the right file when you change cards.