The batch file can be made to execute after the 'exit' button is pressed at the end of the installation extraction using the popular and free Install Creator Pro...

Preparation: make sure your installer copies your modfolder to a temporary folder in the Rome Total War directory. We will call this temp_modfolder

I have explained it here in a more generic sense so that you can see how it mightbe useful to your mod. It is obviously intended for BI mods though may apply to Alexander too.

This is what the batch file does:

1. creates a /mod_name/data folder in your Rome directory
2. copies bi/data into the mod_name/data folder (thus avoiding the copying of other bi modfolder mods that may be present)
3. creates the bi/mod_name folder
4. copies all the contents of the mod_name folder into the bi/mod_name folder
5. deletes the original mod_name folder and all its contents
6. deletes the historical battle folders and their contents in bi\mod_name\data\world\maps\battle\custom\
7. deletes all the files in the base folder as well as the base folder itself at bi\ci\data\world\maps\base\ (NOTE: this step is probably not needed unless you are running a bi modfolder provincial-only campaign)
8. copies the actual mod files in temp_modfolder into the prepared bi/mod_name folder
10. removes the temporary installation folder (temp_modfolder) from which the mod files were copied.

It could no doubt be improved and especially if I could work out how to run a bat file *before* the installer extracts!