Should I disclose that I had cheated on a test and homework assignment in college on my SF86.  Would this issue prevent me from obtaining a top secret clearance or would being upfront about it from the beginning help?

I don't think it is on the 86 but, I was definitely asked about cheating while in college before I was even hooked up to the machine. I think that they observe your body movements and whatever else when you are answering these questions before being hooked up. If they suspect a possible lie, I can guarantee that it will nonchalantly come in in the interview while you are hooked up and just shooting the shit so, they can observe. Then they will bring it up in a formal fashion (let the anal probing begin). There's so much more that goes on before, during, between, and after. After each session (repeated 3 times), I would get home and it would dawn on me what they were doing. Just remember, you are being observed from the moment you walk in.