The term "separation of church and state" derives from a letter written to the Danbury Baptists of Connecticut explaining to them that they should have no fear that the gov't would institute a national religion.
That was in 1811, as I seem to recall, somewhat after the fact with regards to the First Amendment. However, that letter is only the source of that specific wording, not of the concept itself.
We find the concept presented clearly in James Madison's A Memorial and Remonstrance, a pamphlet he was urged to write in 1785 in opposition Patrick Henry's bill in the Virginia Legislature to use tax money to pay for preachers (AKA, "teachers of the Christian religion"). The pamphlet turned public opinion so much against the bill that it died without coming to a vote and, instead, Thomas Jefferson's Religious Liberty Bill was voted into law. And a few years later, James Madison drafted the First Amendment.
A Memorial and Remonstrance presents 15 points arguing for religious liberty and against entangling government and religion. Regarding Jefferson's Wall, here a Great Barrier which defends the rights of the people:
quote:2. Because Religion be exempt from the authority of the Society at large, still less can it be subject to that of the Legislative Body. The latter are but the creatures and vicegerents of the former. Their jurisdiction is both derivative and limited: it is limited with regard to the co-ordinate departments, more necessarily is it limited with regard to the constituents. The preservation of a free Government requires not merely, that the metes and bounds which separate each department of power be invariably maintained; but more especially that neither of them be suffered to overleap the great Barrier which defends the rights of the people. The Rulers who are guilty of such an encroachment, exceed the commission from which they derive their authority, and are Tyrants. The People who submit to it are governed by laws made neither by themselves nor by an authority derived from them, and are slaves.
My page which provides the text of A Memorial and Remonstrance is at http://dwise1.net/rel_lib/memorial.html. Of course, you could do your own search for other sites which carry it along with more of its history.