In options, add a picture editor (Supporting transparency, of course) and then your done. Right click a texture, go to something like "Open" and pick the editor. When your done, click save on the editor, KEEPING THE EDITOR OPEN, open MTE and click save changes. If done right, the texture changed! After a bit of editing or when you want to, click "save pack" and then you've saved it for good.
Repeat until your done with the pack!
Hope this helped. I use this too.
