Maps purchased on SD cards are copy protected and won't work on another card. The backup might be a good idea regardless, because if the card gets corrupted you could reformat and copy the files back to the same card.
On the eTrex there shouldn't be an issue with tracks and waypoints on the card because they are stored internally in protected memory that can't be directly accessed. Your unit might have an option to archive tracks on the card however, so you should be sure that isn't enabled (it is off by default).
Realize that tracks, routes and waypoints are considered "user data" and are completely independent of the map. You can display them on any map that you like.
Buying the map on a card might not have been such a good idea with your eTrex, because that device doesn't have any internal memory for map storage. So that will limit you to using only the purchased map while the card is in the unit. On units that also have internal memory, you could store additional maps there. Or with a DVD version of the map, you could combine it with other maps and put them on a blank card.