Preferences > Tags (2) > Fields (Configure Fields) > Formatting > disc-track# format
HOWEVER!!! In a few places, MB seems to sorts numbers by ASCII instead of true numerical. So you're changing the formatting may still not do what you wish.
No, that's not what I'm after. It's isn't the field format that's an issue. The issue is the prefix number that MusicBee puts in front of the copied files when you tell it to save a list into a folder.
For example, if I have an EP with 3 tracks, with a file name of "disc-track# - title", my base files are:
01-01 - song1
01-02 - song2
01-03 - song3
If I then do MusicBee's Send-To->Folder (Copy) command, the files in the destination folder are:
01-01-01 - song1
02-01-02 - song2
03-01-03 - song3
It's that number that MusicBee prefixes the file name with that I'm asking be made 3 digits when the number of files being copied is 100 or more.