If you hooked up your new stero with the two plugs that weren't attached to the OEM one then it should have nothing to do with it. Of course your going to have to disconnect the amp from the truck and the speakers I think. Not 100% sure though. Try it and see .
I actually found on the internet..some guy who basically replaced the factory sub amp/speaker w/and aftermarket amp and a modified speaker box. It looked like one of those pre-built subwoofers called megaform..or something like that. If i recall i think he bought a rear pre made Megaform (?) enclosed sub for a ford explorer and modified it to fit where the stock sub is in the LC. (they are available in Crutchfield)
I was thinking about doing that someday..just havent gotten around to it.
I am sorry..i dont have the websight. I came across it about a year ago while doing some general stereo searches on the internet. The pic above is basically the same concept as the one i saw..except, this guy used the stock panel to cover up his sub. Only modification was that he replaced the small stock speaker grille w/a bigger one. I will search around..and if i can find it i will post.