"ANIMATED MONSTERS" PLUGIN QUESTION.

I'm having a bit of trouble with this plugin for DynRPG, and I feel dumb because it seems I am one of the only ones with this problem. Since it asks me to make a folder for each monster and to move the png files into it, how do I go about making the background transparent since I'm not directly uploading from the engine itself? I mean, I know how to make alpha channels, but obviously RM2003 accepts a certain kind of color code that makes it impossible.