Use the 'library' --> 'backup' from the menu top left to back it all up. It warns that it is going to take a while, then asks if you want your music backed up (if you have your mp3's on a external drive you can select no) then he is going to backup all the settings, folder structure , cue's and everything to a zip file. This zip file can be restored back.
You're safe this way, every time I add mp3's or set cue's I backup. Easy and safe.