As I have no idea where your video material sits on your site, I cannot advise.
But this has nothing to do with FTP. There are NO static html pages into which you can strip code.
There is no standard add-on (currently) for zencart that will generate a Google Video Sitemap.
So you are going to have to create it manually. Google provides advice here:
http://www.google.com/support/webmasters/bin/answer.py?answer=80472&ctx=sibling
When you have created your sitmap, THIS is the file that you FTP to your server. Again, follow google's advice about what to call it and where to put it and what to do in Google Webmaster Sitemaps manager...