For my dissertation, I tried using Bookends but back then (2008) it didn’t play well with Pages, which was where I finished the diss, and converted it to .PDF for printing and filing.
I ended up using HyperCard (via Rosetta) and Apple Script to place a citation on the clipboard which I would then paste into Pages. This is, obviously, a non-viable workflow these days.
Now, I use a spreadsheet in Numbers. Citations for a humanist a much more straightforward than in some fields; we can generally use in text citations, and a Works Cited, with the first reference to a work cited in a footnote.
My scholarly workflow involve reading a bunch, taking notes on the reading (often by habd, then transcribing) which then evolve into an ur-draft, which may spend time being worked into an outline (if I have to submit a proposal) or worked on in Scrivener’s Corkboard, then as I augment that it becomes a draft in Scrivener. I use the note tools, I import references .pdfs and images, and add notes as I go, I use Scrivener’s annotation tools as I draft. Citations are at this point a FN with a crude citation IDing the author, work, date and page/sections. I dont worry about formatting much, beyond chapters and headings.
When I have a completed draft, when I don’t think I’ll add or remove substantial text, I compile and move to Pages where I revise, format, print out hard copy and mark it up, then revise. I construct a formal works cited at this point, and make sure citations / footnotes are properly formatted.
For technical writing, I use the corkboard in Scrivener and placeholders for figures/screen shots to completely outline the book/article/section of a book including sidebars, call-outs, and figures. I then usually draft in Pages using a publisher’s template or style sheet. Sometimes I have to use MS Word, because of the publisher’s workflow. and macros etc. in their MS Word file. I’ve bought MS Word subscriptions twice because of a publisher’s work flow; the Pages wouldn’t work for productions. I grit my teeth and remind myself it’s still not as bad as when I had to use Quark Express.