So many standards for citation have officially adjusted since I was in school...
You may have a few options in regard to this question (but I would wait for more than this answer).
There are standard publications of confessional material, such as
https://www.fpbookroom.org/acatalog/Westminster-Standards-PB-2004.html#SID=28 The Free Presbyterian Church of Scotland continues to use the unamended Confession of 1646; citation of this in-print publication would direct an interested reader of your material to an easily accessible and authoritative copy. Citations should follow the same conventions as for any other published work, both for footnotes/endnotes and bibliography.
You could also reference an online page of a church or denomination that uses an original confessional document, supplying a publisher's name, link, and the date you accessed the page for your research.
Various churches and denominations have produced their own versions of confessional documents. Sometimes these have edits or amended content, which may or may not be clearly shown within the document. For example, the OPC Confession does not claim to be exactly the Westminster Confession, since this denomination uses a form of the Confession that includes adjustments in the language of several chapters since it was first formulated; rather it is the WCF and Catechisms
as they were adopted. Citing such a document should be done accurately, so that someone using your paper does not come away with a potentially false conclusion about the wording.
As to the presentation, if your paper has an "abbreviations" notice at the start, you might put something there like "2LBC for
Second London Baptist Confession." Alternatively, you might write out the title in the first instance (and indicate in parenthesis your subsequent abbreviation for this source). You could do this in the body of the paper, or in a footnote. Copious references to confessional material might result in excessive footnoting, making in-line citation preferable. Don't use the same abbreviation for multiple sources. Typically, you use chapter and paragraph references in preference to page number, because these are often numbered already within the document. You could use Roman numerals, or Arabic, or a combination (e.g. WCF II.2 or II.ii, or 2:2; WLC 38). Follow a consistent pattern, if possible using the form found in your source.
Sometimes, in order to show the real age of a document you may want to cite an original publication, or one significantly older than one rolled off the press just last year. Many old publications are now accessible on-line just like a library, and you do not need to hold the copy in your hands. The title page looks just like a paper page, and the date/place/publisher are all visible for citation. Sometimes it may be worth a notation in the paper witnessing where you were able to acquire access to such materials (to the benefit of others seeking the same or similar access).
It's typically better to err by including a fuller citation than you may absolutely need. Your professor also may have a preference for the way you cite a confessional source. For instance, one might prefer that you simply quote the material properly, acknowledging the document and place minimally, leaving more room on the page for your work of reasoning and analysis, similar to citing Bible verses. Ask the one to whom you intend to submit the paper what he likes to see.
