As I said, the ONLY way to delete songs from your iTunes library is to select Music under LIBRARY (in the sidebar) and delete songs from THAT list. The iTunes library is your "master copy" and is not affected when you update songs on an iPod.
Doing a Restore is fine, if you want to delete everything. But you don't always want to erase everything...
When you manually drag playlists to the iPod in iTunes, that should only add the songs (not the playlists) to the iPod. If you want to add playlists (that already exist in your iTunes library) to your iPod, it is more convenient to use automatic syncing.
Select the iPod in sidebar. To the right, the Summary screen is shown. Toward the top, there is a bar of buttons starting with Summary. Click on Music next to Summary. This Music screen is where you set up automatic syncing.
Check the box for Sync Music. This setting enables automatic syncing. Select the option to sync Selected playlists, artists, albums, and genres. On the lists below, find and select (checkmark) those playlists under Playlists. (You can also select items on the other lists, as desired.)
When you click Apply, the songs on your selections sync to the iPod. The playlists will also be available (to play from) on the iPod. Going forward, to update songs on the iPod, just update those playlists in your iTunes library (add/remove songs). The iPod does not need to be connected. The next time you connect the iPod (or click Sync if already connected), iTunes updates the iPod with the same changes automatically.