When installing the injection pump, 1st ensure mark 00 on the injection pump gear is in line with 0 on the idle cam gear.
Here are the instructions for a E3AE:
Align the TDC mark to the pointer on the gear case and arrange the notch line on the cam gear so that it is located in the centre of the opening on the cam gear side of the gear case. (1st piston @ TDC). (Note: the crankshaft pulley should have three notches, TDC, 18 and 20 degrees BTDC. These are probably the two marks you are refering too.)
Insert the ingection pump so that the notch line on the rear circumference on the injection pump gear is aligned with the mark shaped like an arrow point over the opening in the gear case.
After the injection pump has been installed on the engine, open the tappet chamber cover of the injection pump and check to ensure the first plunger is in proper position to start injection.
Wear safety glasses and keep yourself well out of the direction of the pump opening for the next segment.
The idea is to have the fuel injected at 19 / 20 BTDC. One way to ensure for proper timing is to remove the injector line from the pump and turn the engine over slowly by hand. When you reach 18 degrees, move slowly through 20 and back. Rocking gently through the 20 degree mark, you should see the pump moving fuel up to you line connector.