Migrating from CCC and an external disk. Would this work?

My macbook Air , OS X yosemite got hacked and I had to bring it back to full restore. It was OS Elcapitan but given the option I restored it to Yosemite. I use CCC and backed up and my storage on my hard drive went from 10 gb to 249 gb, stopped the backup and my computer was instantly not working well. Back to restore to get all that off my hard drive and before I start again. I noticed on my external hard drive that has only been used for CCC backup, it has over 500gb full on it. So, I know I can't put 500gb into a 249gb hard drive. I need to pick and choose or abandon this process all together.

CCC says that Migration Assistant would work. It is not obvious to me.

I am looking for advice. thank you.