You have to put the mod pack name into the user.empire_script.txt file. It's located at C:\Documents and Settings\<user name>\Application Data\The Creative Assembly\Empire\Scripts.
If you don't have a file named user.empire_script.txt, just make one with wordpad or notepad. Be sure to save it as a .txt file. All this file needs is the name of your mod like so: mod <modname>.pack;
The semicolon at the end is important.
For example, my mod is "Semper_Britania", so my user.empire_script.txt looks like this:
Code:
mod Semper_Britania.pack;
And that's all it takes.