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Some hints on deployment:

What I did was to extract the rootfs archive to an SD card and put the uImage to somewhere in rootfs (/boot) so that I could load it by setting u-boot arguments. I still used the stock u-boot instead of the built u-boot, which has a newer version I haven't tested yet.

These are my environment variables for u-boot:

videoargs=video=mxcfb0:dev=hdmi,1920x1080M@60,if=RGB24 vmalloc=384M fbmem=25M

consoleargs=console=ttymxc1,115200 consoleblank=0

rootfsargs=root=/dev/mmcblk0p1 rootwait rw

setbootargs=setenv bootargs ${consoleargs} ${videoargs} ${rootfsargs}

bootcmd=run setbootargs;mmc dev 0;ext2load mmc 0 10800000 /boot/uImage;bootm

bootcmd_fallback=run setbootargs;mmc dev 0;ext2load mmc 0 10800000 /boot/uImage_fallback;bootm

When you insert an SD card, the card will be named mmc0, and the emmc is named (renamed to?) mmc1. /dev/mmcblk0p1 will be the first partition of the SD card. So I passed this to "root" argument. The u-boot command "ext2load mmc 0 10800000 /boot/uImage" is to load uImage from the /boot directory on the SD card to memory address 0x10800000. "bootm" is to start the boot sequence.

I also defined a fallback command to help switch back to old uImage when the new one did not work. You can also modify it to switch back to the kernel and rootfs on emmc. There are 3 partitions on mmc1: mmcblk1p1 is the rootfs, mmcblk1boot0 and mmcblk1boot1 store uboot and uImage. First set "root" to /dev/mmcblk1p1 and make sure other environment variables are set as well. Then run boot command "mmc dev 1;ext2load mmc 1 10800000 /boot/uImage;bootm". (use fatload if the file system is FAT instead of ext2)

I haven't tested it with Mfgtool. I think it should work, but may need some tuning.