I know of 3 ways:
1. Over USB using SAM-BA after pressing the Erase button. This is how we load the initial firmware on production boards.
2. From SD card using the M997 command, usually after uploading the firmware file via the web interface. This is the recommended method for normal firmware updates.
3. Over USB using a fork of Bossa that supports the SAM4E processor (e.g. https://github.com/NorthboundNetworks/Bossa)) after pressing the Erase button.
The first two are documented in the wiki.