I know you need two systems but exactly hows it work? Also I want to buy a co-op games from the Eshop will ds download play work that way or do you need the game cart?
In short, if one is using the Download Play feature for a Nintendo DS or Nintendo 3DS game, the system that is using the Download Play option to connect to another game will temporarily download data so that the two systems can play the game in question together. The data for the downloaded game is deleted when the system is either powered off or returns to the home menu. Although two Nintendo DS systems or two Nintendo 3DS systems will work with no problem for Download Play, a Nintendo DS system and a Nintendo 3DS system will only work together by selecting the DS Download Play option for the Nintendo 3DS, as Nintendo 3DS games can only be played on a Nintendo 3DS system.
As for the matter of purchasing games from the Nintendo eShop, you have no need to worry. The downloadable versions of the retail games are the same as the retail releases of the game, so if the retail release features Download Play, such as Mario Kart 7 or Star Fox 64 3D, the downloadable version will have it as well.