Hi Carole -- thank you for posting to History Hub!
The Annals of Congress are freely available through A Century of Lawmaking -- a website from the Library of Congress that brings together online records of the Continental Congress through the 43rd Congress.
The Annals of Congress cover the 1st Congress through the first session of the 18th Congress. Please note that the Annals were compiled between 1834 and 1856 using the best records available, primarily newspaper accounts. Speeches are paraphrased rather than presented verbatim.
A Century of Lawmaking also has the Register of Debates, the Congressional Globe and the first few volumes of the Congressional Record. You can find the Congressional Record up through today via GovInfo and Congress.gov.
Great question! The proceedings of the 1st Congress are available online. You can consult them here: https://memory.loc.gov/cgi-bin/ampage?collId=llac&fileName=001/llac001.db. Madison introduced the Bill of Rights on June 8, 1789. The House debated the amendments from pgs. 440 to 468. The amendments were then referred to the Committee of the Whole.
On July 25, 1789 (pgs. 685-691), the House changed its mind - it discharged the Committee of the Whole and referred the matter to a select committee. (Some feared that this was an attempt to pigeonhole the amendments.) The select committee ultimately reported; I do not know whether the proceedings of the committee or its report have been preserved.
From August 13-24, 1789 (pgs. 730-809), the matter was again before the Committee of the Whole and later the House itself. This, I imagine, is what you are looking for. The Religion Clauses of the First Amendment are debated from pgs. 757-759. (The brevity of this debate has been a source of frustration for many.) I hope very much that this information is helpful to you, and please feel free to ask if there is anything else you need. Happy research!
Very helpful. Thank you.