You don't structure the HTML in any particular way. You have to tell Kindlegen to generate a periodical using a special flag in the OPF.
see this
bug. I've attached a zip file that has an example book. The .ncx and the .opf are what you need to worry about.
The ncx must follow the format:
Code:
<navPoint class="periodical">
<navPoint class="section" id="1">
<navPoint class="article" id="1_1" playOrder="1">
...