You can use Dreamweaver with Zen Cart, although, with all the modules available, I have not needed to use it and I like to keep things as simple as possible.
There are several integration packages available for a wide variety of CMS systems if you want to integrate it with your chosen CMS. The problem is that several of these integration packages seem to be a little buggy or in some cases, outdated.
I recommend that if you already have a site and are adding Zen Cart to it, simply set up a new file, load Zen Cart to the new file on your server and direct users to your shop. (Zen Cart file). I created a sub-domain on my main site so I have shop.mymainsite.com which works well for me.