Supporting this view of the constitution independence of the States in religious matters, President Thomas Jefferson in 1808 noted:
I consider the Government of the United States as interdicted by the Constitution from meddling with religious institutions, their doctrines, discipline or exercises. This results not only from the provision that no law shall be made respecting the establishment, or free exercise, of religion, but from that also which reserves to the States the powers not delegated to the United States. Certainly no power to prescribe any religious exercise, or to assume authority in religious discipline, has been delegated to the general government. It must then rest with the State, as far as it can be in any human authority.Supreme Court Justice Joseph Story's Commentaries on the Constitution indicate that he also believed the First Amendment left religious establishments in the hands of the States:
It was under a solemn consciousness of the dangers from ecclesiastical ambitions, the bigotry of spiritual pride, and the intolerance of sects, thus exemplified in our domestic as well as in foreign annals, that it was deemed advisable to exclude from the national government all power to act upon the subject. The situation, too, of the different States equally proclaimed the policy as well as the necessity of such an exclusion In some of the States, Episcopalians constituted the predominant sect; in others, Quakers; and in others again, there was a close numerical rivalry among contending sects. It was impossible that there should not arise perpetual strife and perpetual jealousy on the subject of ecclesiastical ascendency; if the national government were left free to create a religious establishment. The only security was in extirpating the power. But this alone would have been an imperfect security, if it had not been followed up by a declaration of the right of the free exercise of religion, and a prohibition (as we have seen) of all religious tests. Thus the whole power over the subject of religion is left exclusively to the State governments, to be acted upon according to their own sense of justice and the State Constitutions; and the Catholic and the Protestant, the Calvinist, the Armenian, the Jew and the Infidel, may sit down at the common table of the national councils without any inquisition into their faith or mode of worship.What is meant by the word "establishment" in the First Amendment? President James Madison during the debates over the ratification of the First Amendment indicated the word "establishment" to mean a governmental religion such as a state church. AS the initial proponent of what eventually became the Establishment Clause, you would think he understood the meaning.
Mr. Madison said, he apprehended the meaning of the word to be, that Congress should not establish a religion, and enforce the legal observation of it by law, nor compel men to worship God in any manner contrary to their conscience. Whether the words are necessary or not, he did not mean to say, but they had been required by some of the State Conventions, who seemed to entertain an opinion that under the clause of the Constitution, which gave power to Congress to make all laws necessary and proper to carry into execution the Constitution, and the laws made under it, enabled them to make laws of such a nature as might infringe the rights of conscience, and establish a national religion; to prevent these effects he presumed the amendment was intended, and he thought it as well expressed as the nature of language would admit.Here are some of the historical facts that brought the Establishment Clause into existence.
First, the resolutions of the State Constitutional Ratifying Conventions from Maryland, Virginia, New York, North Carolina, and Rhode Island, understood in their historical context, all urged a constitutional amendment prohibiting a single national religious establishment.
Second, in response to these State Ratifying Convention's requests, James Madison introduced his original draft of the Establishment Clause which on its face is clearly designed to foreclose a national religion, not religions.
Third, Madison's interpretation given to Roger Sherman during the House's August 15, 1789 debate as to what the House's Select Committee's Report meant (regarding its recommended prohibition "that no religion shall be established by law") indicates clearly that Madison believed Congress was denied the power to "establish a national religion" not religions. 
Fourth, the final wording of the religious clauses of the First Amendment -- "Congress shall make no law respecting an establishment of religion or prohibiting the free exercise thereof" -- shows the intent to prevent a single and no some pluralistic national religious establishment. As Michael J Malbin has noted:
Had the framers prohibited "the establishment of religion," which would have emphasized the generic word "religion," there might have been some reason for thinking they wanted to prohibit all official preferences of religion over irreligion. But by choosing "an establishment" over "the establishment," they were showing that they wanted to prohibit only those official activities that tended to promote the interests of one or another particular sect.
Thus, through the choice of "an" over "the," conferees indicated their intent. The First Congress did not expect the Bill of Rights to be inconsistent with the Northwest Ordinance of 1787, which the Congress reenacted in 1789. One key clause in the Ordinance explained why Congress chose to set aside some of the federal lands in the territory for schools: "Religion, morality, and knowledge," the clause read, "being necessary to good government and the happiness of mankind, schools and the means of learning shall forever be encouraged." This clause clearly implies that schools, which were to built on federal lands with federal assistance, were expected to promote religion as well as morality. In fact, most schools at this time were church-run sectarian schools.It can, reasonably be concluded from this documentation, that regarding religion, the First Amendment was intended to accomplish three purposes. First, it was intended to prevent the establishment of a national church or religion, or the giving of any religions sect or denomination a preferred status. Second, it was designed to safeguard the right of freedom of conscience in religious beliefs against invasion solely by the national Government. Third, it was so constructed in order to allow the States, unimpeded, to deal with religious establishments and to aid religious institutions as they saw fit. There appears to be no historical evidence that the First Amendment was intended to preclude Federal governmental aid to religion when it was provided on a nondiscriminatory basis. Nor does there appear to provide an absolute separation of independence of religion and the national state. The actions of the early Congresses and Presidents, in fact, suggest quite the opposite.
One of the earliest acts of the First House of Representatives was to elect a chaplain. On Friday, May 1, 1789, "the House proceeded by ballot to the appointment of a Chaplain" and "the Rev. William Linn was elected." James Madison was a member of the Congressional Committee that recommended the Chaplain system. Even though the First Amendment did not become part of the Constitution until 1791, if Madison believed in the mammoth concept of separation of Church and State that many attributes to him, Madison would probably have objected on principle alone even before the Amendment was proposed or added to the Constitution. Instead Madison is not only silent on the record regarding chaplains in Congress, he was a member of the Committee which recommended the Congressional Chaplain system.
MORE ON WHAT THE FIRST AMENDMENT REALLY SAYS ABOUT RELIGIOUS ESTABLISHMENT WILL BE FORTHCOMING.
 Paul L. Ford, Life of Jefferson, Vol. 9 (Cambridge, Mass.: Elson and Co., 1904), p. 174. Emphasis added.
 Joseph Story, Commentaries on the Constitution of the United States, 2nd ed., Vol II (Boston: Charles C Little and James Brown, 1851), Sec. 1872, p. 591.
 Story, Commentaries on the Constitution, Sec.1879, pp 596-597. Emphasis added. Story relies heavily on Lloyd's Debates, which are frequently cited for these conclusions.
 Annals of the Congress, Vol. I, p. 730. Emphasis added
 Jonathan Elliott, Debates on the Federal Constitution, Vol II (Philadelphia: J.B. Lipincott Co., 1901) p 553; Vol. III p 659; Vol I, p 328; Vol IV, p244; Vol. I p. 334.
 Annuals of the Congress, Vol. I, p. 703.
 Michael J Malbin, Religion and Politics, The Intentions of the Authors of the First Amendment (Washington, D.C.; American Enterprise Institute for Public Policy Research, 1978), pp. 14-15.
 The Annals of the Congress, The Debates and Proceedings in the Congress of The United States, Vol. I, Complied From Authentic Materials by Joseph Gates, Senior (Washington: Gales and Seaton, 1834), p. 242.
 Reports of Committees of the House of Representatives, First Sess. of the Thirty-Third Congress, in three vols. (Washington: A.O.P. Nicholson, Printer, 1854), Vol ii, House of Representatives Document 124 "Appointment of Chaplains," p.4.