Entirely up to you. I've got nearly 100 cart users hosting with me and every one is in the root.
But if you want a different sales message in a regular type site and the cart in a folder, no problem.
Keep in mind, with few exceptions, the template is ONLY the looks and has nothing to do with the functionality of the cart. Chose the cart that serves your needs then worry about the looks and template.
Presta is new, few templates available.
CubeCart is be far the easiest to change the looks / template for. There are hundreds of free / low cost / and custom "skins" as they call them available. With CC all you do is load the entire skin package to the skins folder and them open your admin and chose that skin from the dropdown list. Truly that simple.
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