Atmel ARM Boot from MicroSD card
The documentation seem to assume that you know what this boot operation mode is about, and why it has sense to be there from functional perspective. Probably it is begin explained and discussed in some Atmel training.

This may also be a historical feature. Look at AT91SAM ARM-based Flash MCU, page 30 - it depicts memory mapping, the very first code block is called "boot memory". As described in 9.1.4 "boot strategies" system always boots from boot memory, and then boot ROM can perform further booting actions from devices and options available.

In your case I bet SD-card is just one of the options to load boot data from  - note that datasheet you point to does not state boot code, but talks about data instead. Probably you can make data to become code so that MCU can execute it. But it is certainly up to programmer if to use this boot feature, how to use data on the external device (SD-card) and where it is located - and all this information should be supplied through the boot memory code which is being executed on power-on (or reset).