[quote name='titanium']You can double register games by doing by creating a sub account. The points for the game registered on that sub account will drop in the main account.[/QUOTE]
To restate this, yes, you CAN register multiple copies of the same game to go towards the same total, you just need to add in additional family members onto the account for each copy you have (still one per family member, though).
To do this, go to the Accounts and Coins link on the upper right hand corner of your Club Nintendo page, next to your coin total amount. On this page, scroll down on the right hand side to the button '+ Add' next to the Family Members section. From there enter in the real / fake information for your additional family member. You may need a unique and valid email address for each family member, but that shouldn't be too hard to come by nowadays.
When registering the additional copy, make sure you log into the newly created username and password, it should still show your correct cumulative coin total in the upper right hand corner.