Boot mode is usually set using the BMS pin on the AT91SAM9 series processors. When pulled down, it boots a NAND flash on the EBI bus. As NAND is expensive and takes a considerable area on the board, the boot strategy was devised relaying on the internal BootROM and a small NVM memory attached to SPI0.
The U-Boot bootloader and a small Busybox are stored there ( for fallback puroposes). U-Boot tries to load the kernel and rootfs from microSD if present, or falls back to the NVM environment if not present.