Dear Sir,
I'm a graphic designer for book cover, book interior, typesetting and layout since 2000. Today, I use Indesign CS5 and CS6. To layout a book, I applied the paragraphs/characters style, object/image style, table/cells style. I guarantee that your styles and footnotes would be keep normally.
I have done several project:
https://www.freelancer.com/projects/Graphic-Design-PDF/Physics-book-design-for-Kusmin.html
https://www.freelancer.com/projects/eBooks-creative-design/Book-File-Creation-Compatible-Ingram.html
https://www.freelancer.com/projects/Interior-Book-File-Preparation-for.html
https://www.freelancer.com/projects/Book-Interior-File-prepared-Ingram.html
Let's we discuss to make a deal for this project.
Thank you.
Regards,
Kusmin