If you have your iPod set to AutoSynch, it will definitely wipe all the songs off your iPod when you plug it in. You'll definitely want to find a way to back up your songs somewhere before try to synch your your iPod, probably the best way being something like Tinkertool (assuming you're in OS X) that will let you view hidden files, like G4ME's suggestion. I think (I'm not a Mac now so I can't check) that iTunes 3 will consolidate your music into the appropriate folders, organized by Artist and Album, so you can copy the songs directly from your iPod and then have iTunes restore the organization of the songs (Your songs on your iPod will be organized differently than on your Mac).