Making Ebooks with lots of math and graphics is a technically challenging problem. The display of mathematics in Ereaders is generally very poorly supported. We have substantial experience in this area. Our native document format is LaTeX. We have been successful in converting our LaTeX documents to the Amazon Kindle, for example. Here are some books that we've converted from LaTeX to Kindle:
If you have math documents written in LaTeX you would like to make available on ereaders, please contact us: Richard Hollos (richard[AT]abrazol DOT com).