There is only 1 TDC when the camshaft timing belt is removed or
the head is off. In other words TDC on the compression stroke
and TDC on the exhaust stroke is determined by the camshaft
position. Camshaft turns once for every 2 revolutions that the
crankshaft turns. You should have rotated the crank to place the
#1 piston to the TDC of its stroke before setting the head back on.
The 5S-FE is a non interference engine so if you have the head
bolted on just install the timing belt and line up the marks. If you
had an interference engine you could force valves into pistons
turning the camshaft if the crankshaft was in the wrong position.