Intake manifold question

Thanks !
Now for something completly different... we changed-out the timing chain this weekend as the vacuum was reading low, 13-17 lbs. When we took the old chain off, the marks were at the top of both the crank and cam gears. So, we put it back the same way. ( one keyway ) I am being told now that the marks are supposed to be together. Wouldn't it not be running AT ALL if the cam/crank gears were 180 degrees off ? Or, did we do the same stupid mistake as the last one to work on this timing chain, and THAT is why the motor has low vacuum ! ( I just can't get it in my head that it could be 180 off and still start and run )