You time the engine by lining up the camshafts and crankshaft gears. There is only one good combination.
I believe you line up the mark on the crankshaft gear with the notch on the block (which should close to the 6 o' clock position) and the camshaft gear marks should be facing each other at 3 o' clock for the intake and 9 o' clock for exhaust. A service manual explains it really well and a camshaft locking tool works wonders.