I'd not bother with the jukebox - its size is tiny.
Just keep them on the card - you have navpro so you have two card slots available to use for music.
I've had two cars with NavPro for 6 years now, never used the jukebox!
If you are getting duplicates, try resetting the index - goto the setting menu, go into factory resets, select just "media" and do a reset - that will rebuild the indexes that are messed up.