One way would be: Most archivers, and archive tools have the ability to append or add additional file items to the original archive. Create your archive with the items you want at the top , then add additional files items to that created archive. I know this works in windows own ZIP tools.
looks like the real answer is beyond me , here for C# http://stackoverflow.com/questions/5898787/creating-an-epub-file-with-a-zip-library
here for HTML (using 7z)
http://next.blurb.com/2011/02/17/how-to-make-an-ipad-photo-book/
specificly this part
2.Open the sample-photo-book folder, and copy the file mimetype into the (empty) archive first.
3.Now, copy the other folders (META-INF and OEBPS) into the archive.
http://idpf.org/epub/30/spec/epub30-ocf.html#physical-container-zip
The contents of the mimetype file must not contain any leading padding
or whitespace, must not begin with the Unicode signature (or Byte
Order Mark), and the case of the MIME type string must be exactly as
presented above. The mimetype file additionally must be neither
compressed nor encrypted, and there must not be an extra field in its
ZIP header.