Every time that I play a tune from my itunes the file duplicates itself into my 'MyDocuments' folder. If I delete this the song is erased from itunes totally. Ideas??
You are of course deleting the tunes from within the iTunes interface.
The settings that I am referring to are your device settings for the iPad. It should show in the left column of iTunes when your iPad is plugged in.
Go through your playlists and make sure that the tunes(s) are removed from any playlist. You can prevent the sync as noted above then do a sync and the iPad should update with the content from you Mac.