I'm not sure what the wiki has to be honest. Ummm... I know how to make map files but..how to explain..?
The wiki is here if you didn't know:
http://aquaria.sfiera.net/wiki/Main_PageDownload The Bear's mod and have a look at the folders/files there. That should help.
http://www.bit-blot.com/forum/index.php?topic=1031.0Put both the extracted files into the _mods folder to be able to run the mod, but I'm sure you both know that already.

When you open the maptemplates folder, thats what it should basicly look like for you. A bunch of black and white png pictures where black is walls and white is space.
So for your mod, make a template like that to work from. Remember that this is the map without entities and stuff, so things like doors shouldn't be put on the template (you wont be able to open them).
Then put them into the maptemplates folder for your mod (if its not there, make it).
Then you need to make a map file to edit. The map file has to have the same name as the template you made (but it will be an xml file not a png

). Instuctions for making map file can be found here:
http://aquaria.sfiera.net/wiki/Modding_Guide:Maps#Map_TemplatesReally, just make an xml file with the right name and put in
<Level tileset="Main" waterLevel="0" gradTop="1 0.5 0.5" gradBtm="0.1 0.1 0.8" gradient="1" parallax="0.5 0.55 0.6" music="YOUTH" sceneColor="1 1 1" />
After that, open your mod in aquaria, load the map you want to apply the template to, and press f11, then 12. Then be sure to save the map. This will make the game edit the xml file with the info of the map that you used.
After that you don't actually need the png template file anymore since the game loads the layout of the map from the xml file. But you may want to keep the templates anyway for easy reference and editing.
To edit a map, just change the template file and then while in the map press f11 and f12 again (or use the menu for it if you want...).