SPECIFICS, MAN, SPECIFICS.
Sue's tileset editor ONLY EDITS TILESET PHYSICS, just so we're clear on that, kay?
If you want to edit the tileset IMAGES, go to your mod's "data->stage" subfolder and find the file that's titled "prt[the tileset].pbm" make a copy of it and simply rename it to a .bmp, ignore the warning message if it comes up, just press OK. Voila. It's a bitmap. Edit it in an image editting program. When done, just save, rename back to a .pbm, open it up in a hex editor (do a forum search on that) and add the "(c)Pixel" to the very end, save it again, copy it back into the data->stage folder, and use it.
And I think I told you this last time, just open up your original copy of Cave Story in Sue's, open the script, ctrl-A ctrl-C it, and paste it back into your mod's Mimiga Village script.