It sounds like the issue you're having is in not replacing a map that covers the game type you want. For instance, if you wanted to put a siege map on, you'd need to replace a current siege map like Fort Boyd - then you select Fort Boyd in game or add it to your server rotation and your map will come up instead.
1-log onto jestservers
2-click on game servers
3-file manager
4-modules
5-Napoleonic Wars
6-scene objects
7-delete the map you will be replacing, for example: arabian harbour
8-Upload the new map, make sure it is the exact same name as the one you deleted. Example:scn_mp_arabian_harbour.sco
9-then go back to the file manager
10-click scenes.txt
11- edit the code on the scene you deleted, and change it to the code for the new one.
12- Delete scenes.txt from the file manager
13- add your new scenes.txt
14- enjoy your new map.
*EDIT* some maps dont need a change in code, the author will usually tell you in his post if it does not.