If your library in either of these is out of whack, then it's the fault of your Mp3s' tags.
The first thing you likely need to do is clean up your files. Try setting it up your file structure as such:
- Music Folder
- Artist Folder
- Album Folder
- [Track Number] - [Song Title].mp3
So, for example:
You may also need to erase all of your MP3 tags, which can easily be done in iTunes & WMP. But with a proper file structure, both will easily self-organize your music library.