If you qualify for the Nintendo 3Ds Ambassador program, your first batch of downloads is ready.
To download your games, at the home menu choose the Nintendo eShop. From the eShop menu, scroll left to Settings/Other and open it. Scroll down to Your Downloads and select it.
From there you can view your free games. They have a Redownload button next to them. Just click Redownload and then Download to get your games.