Hi Steven Moy,
I would suggest you to look into the PostBuild.sh script and modify it to your specific needs. Remember not to include uBoot in the script as uBoot remains without changes.
Depending on what you are updating you can just install the opkg instead of updating everything. The build system is generating an ext4 images so it's an all or nothing type of deal. What you want is something like what some android OTA updates do, just cherry-picks certain files so the update image is small. I don't think the edison build system supports something like that.
Do you have updates in this?
Have you decided how to build the OTA file?