What do you mean by "the kernel on the SD card" and "the kernel from the NAND"?
You can only boot one kernel, and that is determined by your uboot environment settings.
So, which one do you boot from?
If you are booting from your SD card then an update is trivial - you just roll in the new /lib/modules files and update the boot file (uImage).
If you are still booting from NAND the you'll need to update that version.