When you set the timing the lobes on the cam are down and you can rotate back around then the lobes are back up. How can you tell which one to set to

 

I had it where piston was top dead center and the lobes on cam were down. Is that correct?

 

You can install the cam with the lobes up or down. Depends on how you took it apart. Lobes up is TDC on the exhaust stroke and lobes down is TDC on the compression stroke.
I would turn the crank counter clockwise and line up the T mark on the flywheel. Just like you would if you were adjusting the valves. This will put the motor at TDC on the compression stroke. Then install the cam with the lobes down.