Basics

Probably the easiest way to write to content for your epub is to write in markdown, which I would recommend as text based formats are vastly superior.

Probably the easiest way to generate an epub document is to use pandoc.

By using this combination, you get many powerful things built-in.

Frontmatter

http://pandoc.org/README#epub-metadata

The niceties

Page Numbers

One of the questions around the interface between old and new technology is that of page numbers. Should an ebook need to have page numbers? Why? This is a matter of debate For academic purposes, a mechanism to point to the source of an idea or quotation is important, and so I would suggest that some kind of reference system is needed.

In the case of paper books that is the page number and the way in which you can get a page number into your epub has been set out in the guidelines: http://www.idpf.org/accessibility/guidelines/content/xhtml/pagenum.php