I had this problem too. You just have to plug in your iPod to your computer. On the summary, there is a box that says "Manually manage music and videos". Uncheck that box. You now can add and remove music to your iPod without iTunes forcing anything. This also means that checks next to songs in your iTunes Library mean nothying while you are in that mode for that device (if this pressures you, you can re-check that box later). ANYWAY! So once you uncheck that box and click "Apply" in the lower right corner, you then open the drop down menu on your iPod's name on the sidebar and click music. This is a list of all of the music on your device. You now simply delete all of the doubles (this won't delete the songs from your iTunes Library. Your iPod will sync every time you delete a song. Once completed and you see no doubles on the list, you have the option to re-check the box with the automatic downloads (if you want) and your doubles will be GONE GONE GONE!😁
Thank you for choosing Apple.