The separation of Church and State is stupid easy: The State cannot impose laws which enforce religious doctrinal law. The end.
You can pray in schools, at government facilities, express your faith, etc. but no law or enforcement of a faith/practice is legal. This is why there is a prayer allowed at the beginning of every congressional gathering. This is why there were prayers said at the beginning of every school year practiced until the late 60's/early 70's. People only started interpreting that separation of Church and State meant that there was no religious affiliation or association with anything governmental/public until the 1970's when oppressive atheists demanded a change in university practices on college campuses, then it hit the US like wildfire.