Newbie: Footnotes and Endnotes, Compile & Template

Hi. I am currently investigating Scrivener (so, I’m a complete Newbie) for the production of my next book. The book is non-fiction, but the form is more like a Novel (a normal non-fiction popular science book), so I’ve taken the Novel template and removed the Locations and Characters stuff.

I have brought over a first chapter of my existing work for the new book (which has so far been done in TeX using the ConTeXt macros) by importing the PDF and copy-pasting from that PDF to my first chapter (two ‘scenes’).

Now, the TeX book had both footnotes (to appear at the bottom of the page) and endnote (to appear as a special Endnotes chapter at the end of the book). I’ve converted footnotes to comments and endnotes to footnotes in Scrivener.

I have somewhat succeeded using the information in the tutorial and the manual. I was able to compile a manuscript with comments as footnotes and footnotes as endnotes. But I am completely at a loss how to get that effect in a nice PDF output. I am overwhelmed by the behaviour of the compile settings, where for some exports you can output comments as footnotes, and other not. Change the output type and the choices change and I am lost at finding the right combination. I also suspect that choosing the Novel template may have influenced the possibilities.

So, I would like to find out how I can create a nicely formatted PDF with foot and endnotes. I know Scrivener is not a layout program. My previous book (http://bit.ly/1iNacG8) was heavily formatted and done in InDesign for production in hardcover and downloadable PDF, but the next two are different they will have simple layout and mostly text, non-fiction but not a paper or thesis or so, so I was thinking about relaxing formatting/layout perfection for a workflow to produce both print and E-Book (EPUB/MOBI) in one go. If I get this going, I can move from TeX to Scrivener for these layout/formatting-wise simple books.

I have found a solution myself. I found out that the available Footnote & Comments options change based on the choice of Publishing/Proofing for Print Settings. I have (accidentally) found a combination that enables me to export a PDF Proof with footnotes and endnotes.