Yes, I know that SD should work well with El Capitan. Whatever the reason, I was unable to produce a bootable clone although you, and many others, report no issue. I finally gave up and bought CCC.
You are actually the first person I have heard that had an issue. As I stated, the version of SD that came out right before OS 10.11 was released, v2.8 (back on September 20th), worked right away with El Capitan. As I also mentioned, I did not actually move to El Capitan until V10.11.1 was released at the end of October 2015, and SuperDuper! worked fine with it.
I had recently read that OS 10.12 will be arriving in the fall (
http://www.macrumors.com/roundup/os-x-10-12/). What I will do, after insuring that my 5 critical applications work with OS 10.12, is to:
1. Install all necessary software updates for OS 10.12 compatibility (maybe will need to do some of those after installing OS 10.12 in step 6 below).
2. Download the file "Install OS X "(whatever name)"" from the App Store.
3. Go through my weekly disk cleanup/maintenance/repairs, and backup processing for both of my Macs. (This will also insure that I have the file for OS 10.12 "Install OS X ..." on each SD backup/clone.
4. Boot my Mac to that SD backup/clone.
5. Use Disk Utility there to Erase and Format the internal SSD on each of my machines.
6. Run the OS 10.12 "Install OS X ..." installer, creating a fresh, virgin OS 10.12 OS system. That of course will create the OS 10.12 Recovery HD partition (even though I don't need it, unless something drastically changes with TechTool pro).
7. Restart each of my machines from OS 10.12.
8. Use Migration Assistant to "migrate"/copy all the "needed stuff" from the SD backup/clone.
Then, away I go!
