what I meant is when you copied internal to external ssd drive using ccc, you are at this point getting both drives are identical twins. You have to boot up from from external drive (ssd) make sure your cloning and ssd drive is working.
step 1, I assume you are using external enclosure with ssd in it. after cloning with ccc.
step 2, boot up with chime sounds, press 'option' key. then the ssd drive image shows.
step 3 using this ssd to boot up your mac at his point make sure your external ssd is working.
step 4 swap drives out with old in with new.
step 5. boot up your mac, then install osx into your ssd drive,.
since you are using the dual drives, I have no idea what has to be done with the secondary internal drive.
the whole idea is to get your osx in your main drive ssd.
Maybe getting an extra regular drive as external drive after cloning , to get your data using Migration Assistant and not osx to your secondary internal
drive ? Hope not confusing you more.