you should create a new folder, although its easiest to do it through the one click installs and specify a new folder for each
You could also have a new subdomain for each one:
zencart.yourdomain.com or cart.yourdomain.com
I know some people prefer that look, but its personal choice really. Subdomains are a little bit more work I suppose in that you have to set them up first (although its not much work).
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