NOTE: If your mod is loading fine, but you're not seeing your changes in-game, read
The ETW/NTW engine has a built-in mod loading method that allows you to switch packs on and off. This doesn't really have an interface but the switching is done by creating a file called user.script.txt in your scripts directory and entering the mod packs you want to load into them.
So, first set your mod type to "mod pack" by right-clicking in PFM, go to "Change Mod Type" and select mod pack, then edit something and save. Be sure to copy the name of your pack file, including the extension, for example I have a file for testing purposes called "alpaca_1.pack".
Then navigate to your scripts directory, in ETW it's in "C:\Documents and Settings\<username>\Application Data\The Creative Assembly\Napoleon\scripts" (I forgot where it's in 7/Vista). Then copy preferences.script.txt and rename the copy to user.script.txt.*
Open the file in Notepad or another text editor, remove all lines and add a line like this:
Save and your mod pack will be loaded by the game. For each additional pack, add another line. I always use quotes and you have to supply the semi-colon ";" at the end of each line.
If you add another pack further down, any files in that pack which have the same name as a file in a pack above that, or a vanilla pack, will override
the copy from the above pack, i.e. the file in the last pack that contains it will be used.
Additional info: you can put any settings you have in the preferences.script.txt into the user.script.txt which can be useful because the user script is not overridden when you save options in the game. I have a user script for testing that has windowed mode enabled and uses a lower resolution, and a user script for playing which doesn't have these settings. You'll have to rename the one you want to use to user.script.txt when you start the game.
* Copying preferences.script.txt will automatically make sure the new file is saved with unicode encoding, rather than ANSI which is the default when you create a new text file. So it's the easiest method to create a user script.