It should have the same structure as your game/server files.
Ex:
http://www.dfsdfsdf.com/FortressForever/maps
http://www.dfsdfsdf.com/FortressForever/materials
You need to put any custom maps on your Fast DL in the same directory that they are in on your server. A few custom maps out there come with custom textures so it's best to DL the map.zip so your sure to keep the structure and all textures that the map needs. Also it would be better to convert to .bz2 format.