Hi,
It depends how you are trying to rearrange them and how you are playing them - by album or by playlist.
If you play from the Phatbox using artist/album search then you must modify the tags of the files that specify the track number. You mention PMM, but you do not say if you use Phatnoise Music Manager or Phatnoise Media Manager (I use the latter which has a pretty good tag editor). The way that I would use this to change track number tags is first to create a playlist, and put all of the files required into it (from any albums you like) in the desired order. Then select all of the tracks so that they are highlighted. Then right-click on the tracks and choose "Edit file tag". Select the "track" tick-box and then select the bottom item in the track number list - "Auto". Then click Apply. The software will then rewrite the track number tags for all of the files in the playlist in the order that you have placed them. It's a neat trick and it has its uses, but personally I would leave them alone and do it this way instead...
Alternatively, if you want the files in an arbitrary order you can rearrange the order of the files in a playlist and then the playlist will be saved when you sync the DMS. But then you must only select the files by the playlist search when playing them for your wife, otherwise they play according to the track number tags.