I've moved this thread to Plugin Support. Thank you.
In the thread for the plugin I give instructions to create two versions of your tilesets. One is the larger 48x48 version in the default folders that is used in the editor, and the other is the smaller 32x32 (or whatever) version that you want to appear in-game, and the images for that are in a subfolder.
There is no way to change the editor to use tiles of a different size.
You could also have posted this question in the plugin thread.