Which Icon do you get using the fork at the hot spot on the roof? If it is the Green flying wings then you have already knocked the skull piece into the chapel, if it is the Green pulsing circle then you have not managed to get it yet. On my system there was an audible and fairly loud "Click" when you popped the skull off the cross.
Inside the chapel it should be in the pathway before the alter. At this point it still looks like a piece of bird doo rather any a piece of skull, but it should be the only brownish-cream colored item on the floor in the walkway.
Hope this helps,