svwilbur,
You are right on in your thinking...if you install the distributor a tooth off either way, it doesn't make a bit of difference as long as you can rotate the distributor enough to make up for it. The vacuum advance usually limits this rotational travel as well as the cut length of the plug wires. Sticking it back in the 'right' spot is for your convienience...so you have equal rotation either way.
I'm not sure what your manual is trying to say! There is Before Top Dead Center, BTDC and Top Dead Center, TDC and After Top Dead Center, ATDC, but that about covers all the bases.
If you chalk the timing mark on the crank pulley, pull #1 plug and tap the engine over with the coil wire removed, you will hear air rush out of the plug hole and you will see that chalked timing mark rolling up to the timing tab. When it on 0 degrees, that is TDC.
Stuart