Focus Stacking with Zerene Stacker
You can use a Zerene Stacker from Zerene Systems to create the final stacked composition image from your Focus Stacks. ControlMyCanon has an option to automatically export the captured stack to Zerene Stacker.
This is really handy because capturing a large stack and processing it can take a good amount of time (up to an hour). So with ControlMyCanon and Zerene Stacker, you can start the focus capture, wander off to do something else and come back to find the complete and processed stack on your computer monitor.
(shows ControlMyNikon, but functionality is the same in ControlMyCanon).