First of all, go here for a guide of what file is what and the location:
http://ffxi.killvoid.com/page.php?id=250&PHPSESSID=f838dd61504628e85c78acd1a0384583
Then, before you replace the specific file with your new formated music file, simple copy (or move) it to a new directory. For example, C:\FFXI Music Backup
After you modify the sound file to fit your needs (remember, you may want to edit it so it fits in a loop well), you convert that MP3 into a BGW file (using the utility....everything you need should be in that guide) and just rename it to the appropriate name. After you have the original file(s) backed up (or copied... or moved), simply rename the replacement file. I.E. if you're changing the Mog House music, it's music126.bgw so you'd rename the new file to music126.bgw.