For your music, make sure it is all tagged including the album artist tag, media centre depends on tags to organise the music. I use an application called mp3 tag tools to tag and rename files as well as album art fixer to tag and download album art.
Install My Movies, this will help you to organise your DVD's and VOB's.
If your mp3's are tagged ok it does not matter what folder structure you have, but for ease of finding music (when copying and ripping in explorer or other apps) why not create a folder called artist name with a sub folder of album title?
Steve