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Yes, I reserve H1 for the book title.
I've tried various things with footnotes: (1) Adding them in [square brackets] immediately after the text which they are noting; (2) Adding them at the end of the chapter and linking them from/to the main text; (3) Adding them to separate footnote file/s at the end of the book and linking them to/from the main text.
(1) avoids links and is fine if the note is short, otherwise it can be intrusive.
(2) is good for short to medium length footnotes.
(3) is good for longer footnotes.
I'm not sure what you mean by annotations.
I use limited imprint data and include it on the title page and I also include an inline contents page after the title page - usually just listing the first levels of toc.ncx. (This is probably a hangover from printed book layout and may be redundant.)
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