You want to set the timing to the spark mark.  The rotor should be in the Mag window when number one cylinder is near the top and the spark mark is at the center of the hole for timing.   If the rotor does not apear in the window when number 1 is at TDC, one of two things could be wrong, the mag is 180 degrees off, or the flywheel was installed 180 off which is possible to do!