Format during each new install. Only clone with images you made after you're done setting up your PC (eg. stuff like installing chrome, word, etc).
I also would not clone from a HDD due to it having so much crap on it that isn't healthy for an SSD.
You still can booth from both as long you have an OS on it. If you wiped your HDD after getting your SSD up and running, no you can not boot from it again. At least not until the point you install windows on it.