Having never used EZ populate I can't comment.

But with regards to your questions on html, the template system in Zen Cart allows you to replicate almost any look that you wish, using the header and footer tpl overrides combined with the css, almost anything is possible.

Note: If you have an existing html site, you can use most of the existing html to build you header and footer of ZC site.

The easiest solution would be to let ZC become your site, using EZ pages for non cart related pages. It also makes management a lot easier as everything is in one place.