If you want to install the Mod and keep the ability to switch out to a stock version of the game, you have two options.
You can download the JSGME version of the Mod which includes the JSGME mod enabler that is very popular in the SHIII community which can automatically install and uninstall the mod.
You can also download the mod by itself, there are two separate distributions available, make backup copies of your stock Database and Doctrine folders (which is recommended anyway), btw they're the only folders edited in the LWAMI Mod, and copy them back over the Modded folders if you want to restore the stock game.
So basically, since the mod only edits things in the Doctrine and Database folders, changing modded and unmodded versions is as easy as changing the folders.
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