After you have altered the texture, you can do new MAT file for your new texture. Take a copy of the "old" MAT file, open it in a text editor and replace the filename (and possibly path) from the old texture to the new one. Can easily be done with a "search & replace" command found in most text editors. Or, even easier, download the MAT Pose Editor form free stuff and use that to adjust the MAT file so that it loads your new texture.