Thats not exactly what I was asking, however, I discovered the answer on my own.
I wanted to know how to move the FXFactory Plugins to my new installation of AfterEffects CS6 without having to re-install FXFactory. Since the plugins are not in the AfterEffects Plugins Folder, I figured they had to be elsewhere.
You need to goto the library at root level, not user level.
To get there, select your Macintosh HD>Library>Application Support>Adobe>Common>Plugins>CS5.5 (or CS5) >Mediacore>
Move or Copy the FXfactory.plugin and ImporterFxFactory.bundle from the CS5.5 Mediacore folder to the CS6 media core folder.
That should be it.