This feature won't be available until a future update, so we don't have all the details just yet. Until this feature does become available, there are a few things you will want to keep in mind:
When the transfer feature becomes available, you will need both your Nintendo DSi/Nintendo DSi XL and your Nintendo 3DS to complete the transfer. This is because the transfer of data will occur via local wireless communication.
Data cannot be transferred to another system over the Internet, using an SD Card, nor can Nintendo complete the transfer for you.
More information on this process will be available on our support site and at www.nintendo.com/3ds once it becomes available.