Storage in embedded linux
As is the same with Linux on full-size machines, the bootloader passes the location of the root as the root argument to the kernel. The bootloader itself (usually Das u-Boot) is responsible for checking NOR flash, NAND flash, SD, USB, SATA, PXE, etc. to see if a kernel and optional initrd can be found, and passing options as defined in the board's environment variables.

TL;DR: Check the bootloader configuration and kernel command line.