If you are in this situation you basically have three choices. One, you can choose to continue automatically updating songs and playlists, but choose to update only checked songs (indicated by the check mark to the left of each song title in your iTunes library).
Or two, you can choose to automatically update selected playlists only (and select only as many playlists as will fit on your iPod). Or three, you can choose to manually manage songs and playlists, copying songs & playlists over manually in iTunes by dragging & dropping them onto your iPod in the source list.
Each of these options can be selected in the iPod Preferences in iTunes (with your iPod attached to your Mac, select it in the source list, and then click the iPod icon button on the lower right).
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