No need to pull the valve covers. The marks we're talking about are the one's located on the belt pulleys (the one's you were trying to get aligned to start with). I don't thing there is anything under the valve covers that is going to help you with the alignment.
I remember reading about dots on the camshaft gears lining up under the valve cover but like i said before i think each of the camshafts spring into only one position. So im pretty sure removing the valve cover is NOT necessary...