Adding separate backup section on clone disk with OS

First, I'm new to using TIH, I have 2012. I have a new 90G SSD on which I will load: Win7, a 3D CAD program, and MS Office (under 25G total). I want to clone these to a new 120G SSD (I don't trust SSD's yet), and use, more or less, the remaining 30G for backup files, assuming the cloning takes about 90G. So, can this be done in some manner? I'm not sure how the OS and apps on the clone ("secondary") wouldn't be seen while using the primary drive OS and apps if the secondary drive is active (power/sata cable) for backup. Can this be accomplished thru partitions, and not having the cloned apps partition active? Or something? I'm a user, not a disk guru. I need step by step.