Here is a picture I made to help understand the cycles of the engine.
As you can see, when #1 is at the timing point (overlap TDC), #4 is at TDC on the compression stroke. So the cam settings will always be 180 degrees out of phase. If you set up with TWO dial indicators you should get the same reading on each bank-- nail it on #1, then turn the crank 360 degrees and nail it on #4.