To answer both of your questions:
Yes, MSS can be applied by hand but it's very difficult to get a thin, even application. It's best applied with a machine since it's much easier for a machine to apply that thin, even coat. If you have heavy spots (which are inevitable when doing it by hand) they can be tough level out after it hazes and you begin to remove the residue.
Quick Sealant is a better option if you want to apply a sealant and don't have access/own a machine. That's the very reason we formulated it, for those who want to seal their paint but don't have a machine.
Regarding the scratch, you can most definitely polish only that area. Our 4" focus pads come in to play perfectly here, especially when used on a cordless drill. They will make quick work of scratches, provided the scratch isn't through the clear coat. If you can catch it with your fingernal, then it needs something a little more serious to fix it.