To make a new extension you need the squashfs-tools-4.0 extension installed.
Create a directory for your new extension. For example:
mkdir -p /home/tc/myext
Copy directories and files to myext. You must include directories. For example, if your file is in /usr/local/myfile use /home/tc/myext/usr/local/myfile.
To make a new extension:
sudo su
cd /home
mksquashfs myext/ new-extension-name.tcz
Paste the new extension to the /tce/optional directory.
If you want it to be loaded when you start the computer, add it to CPanel -> Apps Audit -> On Boot.
If you want it to be available on demand, add it to CPanel -> On Demand.
If you want more than one extension to be loaded at the same time, create a .dep file with the names of other extension(s) to be loaded. (If you run CPanel -> Apps Audit -> Dependencies -> Update Dep Database, the .dep file will be removed, so save a copy to put back after running it.)
If you want it to be run when you start the computer, add it to CPanel -> Apps Audit -> On Boot, and add the start command to /opt/bootlocal.sh.
Once you understand how to make extensions, if you use persistent home and opt, and make extensions for anything else you want to save, you don't need to use backup.