Brain Fertilizer

The kerfuffle over the words "under God" in our Pledge of Allegience has brought out all sorts of opinions regarding the role of religion in our society. In my opinion, the atheists are grasping at any opportunity to eliminate the practice of religion or appearance of religious symbols in public. Several people cite "separation of Church and State" as if it were in the US Constitution, rather than being an opinion of Jefferson mentioned in a private letter, somehow dredged up and turned into law by a 1950s era SCOTUS ruling.

So here's my question: Does every SCOTUS ruling interpreting the Constitution become equal to the Constitution itself? If legal precedents by different judges can end up turning the Constitution against itself, is there any system of priority? For instance, the "Separation of Church and State" precept is rather vague, in that some people seem to think it is wrong for President Bush to use his religious belief and faith to guide him in his decisions as President. It would seem equally plausible, then, to prevent ministers/pastors/priests from ever running for office. It could then be equally plausible to prevent ministers/pastors/priests from voting, because they would be using religious values to affect government...

But, clearly, the separation of church and state was supposed to ensure that religion wasn't affected by the state, not the other way around. At the very worst, if one isn't forced into saying words or participating in a religious rite, there is no "establishment" of a religion, right?

Anyway, the point I'm ever-so-slowly rambling toward is:
Shouldn't the Bill of Rights take precedent over later Amendments? Shouldn't Amendments take precedent over Judicial Rulings? And if that is correct, where does the Bill of Rights stand in relation to the original document? Slightly higher? Slightly lower?

Help.