Nintendo posted a how-to on its support page, and ... a lot of people are going to need it. In order to get your free games, you'll have to open up the eShop (cool so far), then ... go into the "Settings/Other" menu there, scroll to "Your Downloads," and then click to "redownload" each game, even though you're actually downloading them for the first time.
Sounds kind of crazy, but our guess is that Nintendo has opted to add the games to everyone's accounts as already having been purchased, rather than generate codes for specific games. We're not even sure it's possible to distribute a download code for a 3DS game.
But it gets crazier! In order to keep up with news related to the program, Nintendo will offer the "Ambassador Certificate" for download -- which is actually a video. You'll be able to tap icons during the video for updates about when games will be available. Alternatively, read Joystiq!