One very important thing to me when looking in factual reference books, is the Source reference.
We may not be interested in looking at your family document sources, but reference sources can be very valuable to others (especially if we didn't know they existed, or how useful they might be), for using those sources in our own research.
Don't forget your Archive places, the collection name with reference numbers, with folio / page / sheet number and date; or Book title, pub. date, with the page number.
My feeling is that these MSS / document / Will / newspaper / book / if GRO Cert / Inquest / Divorce / Inquisition Post Mortem re land ownership / Manor / Tithe document / Act of Parliament / Court case / Grant / Letters Patent or Arms (if any) footnote references, are best at the bottom of the relevant page.
Say if it is word of mouth (passed down), or by letter to the author from Mr Nobody of Haslemere, nothing worse than searching archives that you think may hold the information, to find it is not there and concluding that it must be the author's own knowledge, or source is left unknown.
I hate references that are at the end of the chapter, or end of the book by chapter, as I often can't remember the chapter number I'm reading, have to thumb backward to find the chapter number, then find either the end of the chapter, or go to the back of the book and find the relevant chapter and then thumb down to the footnote number for the reference, by which time I've forgotten the footnote number, by the time I've got there.
If your references have to go at the back (because you are not sure how footnotes will work with page layout) don't start with footnote 1 for each chapter, but carry the footnote numbering on, from the last chapter.
So you see footnote 256 and go straight to References at the back (without having to work out which chapter you are in) and thumb straight down to 256 and the document of origin.
Mark