Yes, you will have to lock the crank at top dead center (TDC) on the power stroke with both valves closed. There is another TDC between the exhaust and intake strokes, but that will give you false readings because of cam overlap holding the valve open. In other words, the exhaust valve is not quite fully closed and the intake valve is beginning to open.
Actually, you may need to be part way down the cylinder on the power stroke to be sure the intake valve is not on the compression release, depending on which engine it is.
Before you put the head back on, roll the engine over to TDC on the power stroke and see if you can turn either valve with your fingers. if you can spin it, its not closing fully.