Thought I would share my recent experiences as a sorta GPS newbie who successfully got nice topo maps and AT waypoints with shelters onto his Android 2.2 smartphone for free! (HTC EVO phone) This may help other noobs. It took a few hours of time and about 2 gigs of space to get 500 miles of trail downloaded to my phone. This means I don't need to be wifi or celltower connected to use the maps, phone can be in airplane mode, thus saving batteries and not relying on connectivity for usage, and GPS can be used regardless. My method might be exhaustive for someone doing the entire trail, perhaps better for section hiking, but below I will discuss some options for thru-hikers... I just start rambling this out!

I tried a bunch of apps. The best functionality seemed to be OruxMaps:
http://www.oruxmaps.com/index_en.html
It is free, but I'm sure donations are accepted!
On the Manual page you will find a link for a pdf "how to make maps from scratch":
http://www.oruxmaps.com/manual_en.html
http://www.oruxmaps.com/oruxmapsdesktop_quick.pdf
In the instructions you will find you will need to install Mobile Atlas Creator 1.8:
http://sourceforge.net/projects/trek...8.zip/download
You don't need to "install" it just unzip it and put it somewhere on your computer. Windows only I assume.
I mostly just followed the PDF instructions...
For map source I used "TerraServer USA" it has nice topos.
Each map I created was about 200 miles of AT trail, you could go larger with each map but each download operation will take longer, and the square that create gets unnecessarily large, the smaller the map, the smaller the rectangle - the AT obviously moves diagonally across the US usually so you end up with these unneeded areas in the map rectangle, but I guess those areas tell you about the towns available for emergencies. To select the map, I used "google maps" as the source because its easier to see the towns. After selecting the rectangle I switched to TerraServer.
Very important - when setting up the map, I chose a maximum zoom of 15. If you choose 16 its too many tiles and too much memory! So choose 15, as well as 13, 12, and perhaps 11 and 10 etc. The smaller the zoom the less it matters whether you choose because the smaller zooms take up much less tiles. You can see the tile count change as you select them. Once you get over 20,000 tiles in a map it starts to take a long time. If you were hiking the entire AT you save yourself alot of time and memory and get a maximum of zoom level 14. Select 14,13,12,11,10 and you could probably get the entire train onto your phone's SD memory card in a couple Gigabytes.
Name the map something useful like "springer-erwin" and create atlas.
Once the download completes, and after you've installed OruxMaps on your Android, plug phone into your computer and copy the entire directory "springer-erwin" to your phone, I think the directory was something like "/oruxmaps/mapfiles". You will see "world" directory map already there.

Other stuff...
This site can help with planning all kinds of things, including the map rectangles you are creating:
http://sophiaknows.com/atdb/atplanning.html

Shelters and waypoints:
This site has AT trail and shelter data from I believe 2003 or so:
http://guymott.com/atgps.html
You can download the .GPX files and import into your OruxMaps Android app so you can see the trail and shelters on top of the topos you just downloaded. You can experiment with various GPX files that are available. The .GPX files (not the zip files, unzip them first) go into a folder on your phone called something like "/oruxmaps/trackfiles". Keep in mind OruxMaps can't access files on your phone until you take it out of "disk mount" mode or whatever its called because the SD card won't be available to apps, so to test after copying files you must put it into "recharge battery" mode or just unconnect it. After you copy the GPX files there, you can goto "tracks" from the menu and then "import track", select the file. Once it finishes (large tracks may take a while be patient) loading you have to select it and load it for it to show up on the map. I found you can load the shelter file as a "route" after its imported, because you can only have 1 track file loaded at the same time. So if you load the shelters as a route and the trail as a track, you can view them both at the same time on top of the map!
I downloaded the track files of the trail the were filtered at 50 feet, seemed about the best size. I also found that performance was much slower if you downloaded that one all at once. He also offers the 50ft file as a zip of 40 or 50 different files. You can import each of those independently and when you have them on the map one at a time it seems much better performance. Perhaps the 200 ft filtered track would be easier to get the entire thing loaded at once at still have good phone performance. Perhaps I will try that myself also.
Of course once you are out on the trail you can use the maps like a normal GPS device. This is incredible today for an Android phone to be used much like a Garmin, and all the maps and the app is FREE.

I hope this isn't confusing, if it sounds very very confusing then perhaps this is not the thing for you. If you are an Apple user with an iPhone there is probably another way to go entirely. I am a GPS newbie and so if you are not then this is probably not that useful for you either. Good luck!

QWERTY