To clarify the previous answers a little bit, you can think of Maemo Mapper as able to run in two different modes: with Auto-Download enabled or disabled.

With Auto-Download disabled, then before you embark on a trip, you must download all maps that you anticipate needing for that trip. There are two ways to do this: with an external program like winmapper, and with the "Manage Maps..." menu item in Maemo Mapper itself.

In the case of the latter, you have two options. You can download maps "by area," in which case you provide the latitude/longitude of the corners of a rectangular area, and Maemo Mapper will download all of the maps in that rectangle. Or, you can download maps "Along Route", which means that, if you have a route loaded (i.e. directions to a location), then you can download all of the maps that you would need along that route.

With a large enough memory card, you can conceivably store entire countries at a decent resolution. To maximize the effectiveness of your memory card, though, I recommend downloading maps around your home at a high resolution, and downloading maps further away from you at a lower resolution.

With smaller memory cards, it probably makes more sense to just plan each trip in advance and use the "Download by Route" feature. This will minimize the amount of memory card space needed at one time, but it reduces flexibility because you won't have map data for areas outside of your route. When you are done with your route, you can delete all your maps to save space and/or prepare for the next trip.

With Auto-Download enabled, Maemo Mapper will download maps on-the-fly as needed. This eliminates the need to pre-download large areas of maps, but it requires an active internet connection at all times. If you're using Maemo Mapper in the car, that usually means connection to a cellular service with a data plan. Note that Maemo Mapper will still cache the downloaded maps for you, to minimize internet access, so if you want to keep your memory card free of excess maps, you may want to clean out your Map Cache every once in a while.

I'm sorry it's not more intuitive. This app is in serious need of documentation! But I hope this helps.