It works without any extra programs with the EZV but you can use it with any other card using Rudolphs 3-in-1 tool. a 3in1 + a M3DSS/R4 is a very popular combo/
You can run the games from the temporary storage(PSRAM) in seconds, provided its not over 16 MB(128Mbit). If it is you have to burn the games to the NOR storage, Which is similair to how the old GBA flashcards work.
Only 1 game at a time though.
Flashing to NOR must be the storing of gba games youre talking about.
You can also patch games and then flash them to NOR so you have NDS/GBA connectivity
This has been confirmed to work with Pokemon using a patch that can be found here
http://ezflash.sosuke.com/about5342.html
The post by cory1492 has the patch i believe