Hello Tdavis,
Yes, you can certainly use the ZenCart in conjunction with the web builder. You will want to install the ZenCart using the Fantastico installer tool via your cPanel.
When installing the ZenCart, ensure you place it in a subdirectory so it does not interfere with the builder pages. To do this, simply name a folder you want to place your ZenCart at the 'Install in Directory' field when using the Fantastico. The folder cannot already exist as Fantastico will create it. Normally names like 'store' or 'shop' are used, but you can name it anything you like.
To attach it to your builder you will need to go to the builder Step 3 (Pages) and select a speical page named "External Page". When you edit that page on Step 4, you will simply enter the URL you set your ZenCart to (for example http://domain.com/store). This means when someone clicks on that link in your builder site menu, they will be taken to the ZenCart portion of your site.
Best Regards,
Scott M