AgoraCart running while building my new store? Sub-folder install possible?

I currently run AgoraCart on my domain for my online store (www.farmersapothecary.com). After some research into its features, I'm really thinking I would like to switch to using Zen Cart. Would there be any foreseeable issues to installing Zen Cart into a subfolder on the domain, and building the Zen Cart driven shop while leaving my AgoraCart shop running until I got to a point where I could make the switch official? I've been reading through the site, and found a tutorial on moving the cart from a subfolder to the root, so that seemed pretty straightforward. I'm mostly worried about breaking my current AgoraCart by installing Zen Cart on the same domain.

Thanks in advance!

Sounds a good plan. Make sure that the public can't find it.
You can test the zen-cart until you feel ready to go live.
There is lots of info available in the faq's and the tutorials that will help you.

We set up zencart in sub-folders on many, many sites - including Joomla, Wordpress, Drupal ...

As long as you keep it all in its own folder / directory it will not interfere with other platforms.

In most cases, we set a folder password (htpasswd) which blocks unwanted visitors, including SE spiders.

Cool. Thanks much guys! :)