Timing

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.