Each time you want to test your tileset in JJ2, you must do a certain thing: Move all the colors in the palette you just created to the right two entries, because of the transparent colors, and take care of the fact that all pixels with the color 0,0,0 are changed into something like 0,0,4.

If you test your tileset often this can be annoying and errors happen easily(like missing a pixel, etc) Perhaps a program could be created that does a thing like this automaticly. As an extra, maybe it could allow you to re-arrange the tiles in your bitmap(I am not talking about .j2t editing!)