Temporarily, one will be named MnSlChr.usd (the program will work on this file when you use it), and the other can be named anything. Use the music manager to work on that file, then, swap the names of the two files, then use the program again; so the program should then do the same thing to the second file. When you're all done, one should be named MnSlChr.0sd, and the other MnSlChr.1sd (doesn't really matter which is which, but .1sd is the one normally used as the one containing the Tri-CSPs; if you reverse them, the Debug Menu option regarding Tri-CSPs will also be reversed).
Alternatively, if you know how to use a hex editor, you could copy the modified hex from the first file, and paste write (not paste insert) it into the second file. You could diff your original MnSlChr file with your modified one to see what area needs to be copied. If you don't understand this part, just use the above file renaming method.