- Your files you mean? You tag the files in mp3tag. Drag them into iTunes. And same tags appear there. If you make any more changes to the file in mp3tag then you have to play the file in iTunes for them to update.
What do you mean 'reorganizes my tags without asking'? Personally I don't care what what the files look as long as iTunes reads the tags properly. iTunes is way more powerful internally by means of smart playlists and organising music than windows explorer will ever be.
If your worried about iTunes leaving behind empty folders see /t/13629/1