TDC = Top Dead Center: By definition, the piston is at the top of it's stroke. The piston will not be down. The flywheel is tied directly to the crank, so the piston can't do something different from revolution to revolution with respect to the TDC mark on the flywheel.
What may be confusing to you is the fact that the camshaft speed is half the crankshaft.
Don't worry about the rocker arms right now, because you are just now installing the cam. By lining up the marks like you described (which I'm assuming is from the manual... I didn't verify what you said) you are establishing the proper phasing between the crank and cam so that the valves will open and close at the proper time.
The trick about checking if both rocker arms are loose is to confirm when the piston is at TDC on the compression stroke. You need to do this when you set the lash on your rocker arms. The rocker arms are loose because on the compression stroke, both valves need to be closed, so the cam is not pressing on the arms at all. The other time the piston is at TDC will be at the top of the exhaust stroke, in which case the exhaust valve will be open (so the rocker arm will feel tight).
- Frank
1984 200ES Big Red
1985 350X (x2)
1986 350X
1986 250SX
1984 Auto-X
1984 ATC70
1985 ATC70