You're right about not being able to change the font size for the headers and footers, Orion. But I'm glad that the underlining problem is sorted out.
As for the chapter breaks: BD generally starts a chapter on a new page if you have labelled the chapter title as a "title."
However, if ever you have a very short chapter - say if you are converting a book of poems - then BD tends to skip at least some of the pagebreaks.
Harry and I are both tidy-minded, so we make sure that all the pagebreaks are inserted. This is also a useful thing to do if you are planning to convert the book into other formats, or to make a mobipocket book (via Mobipocket Creator) from the BD source.