Hope this is what you mean because I don't think you've actually specified which mod you want to load so this is how NovaLogic does it.
You'll have to point the game shortcut to your mod pff. by adding the argument /exp jox01
For example...
The JOTR expansion (JOE) is a PFF file located in a subfolder of the game, the path to the mod is expansion/jox01
JOTR
Code:
"C:\...\NovaLogic\Joint Operations Typhoon Rising\Jointops.exe"
JOE
Code:
"C:\...\NovaLogic\Joint Operations Typhoon Rising\Jointops.exe" /exp jox01
Find the mod pff and try loading it the same way