i have done this following instructions to boot from SD card :
Boot the system | ConnectCore 93 (digi.com)
but it does not work.
i solved this problem after doing the following 
- List item do not change the the micro-switches (SW3) they should all be off to boot from eMMC.
- in the .sdcard.gz` file will create two partitions in the SD Card . one contains the boot files and the other the Kernel image.
- you have to run the boot.scr in the SD Card
you can do it by doing the following
- fatload mmc 1 $loadaddr boot.scr
- source $loadaddr
- after that you have to shutdown and power off the device. and change the SW3 as described in the link.
****** if you booting you custom yocto image you have to do the following
