I would recommend looking at installing the Generic Mod Enabler (JSGME), it is a brilliant little piece of software that is a huge asset to modder and casual gamer alike. I have used it successfully in
AJE,
BOR,
PON and
WW1G in addition to a number of other games.
J Scones Generic Mod Enabler
Follow the JSGME installation directions closely, create the "snapshot" of the stock game and then you can swap the modded files in and out as desired. You may need to make sure that the file path for the mod is identical to that in the stock game but that's pretty easy to do. Most people who have issues with JSGME have not read or understood the instructions, which are very well written and complete.
JSGME overwrites the files in the game with the files that you place in the Mod folder using a simple interface.
Make sure to roll back the game to stock BEFORE applying any updates however.
Good Luck.
-C