Zencart (like all generic carts) cannot be "sliced up" and used piecemeal. There are almost a million lines of code in a comprehensive installation - all dependant in some way on each other.
And embedding into a frame is a no - no . Payment gateways will reject a pass from an iframe and you will also encounter serious session issues.
Session issues will also be a problem if you "house" zencart in a sub-directory as these are timed to expire (for very valid security reasons). Basically, this means that if I am on your site, adding products to the cart, and I get distracted into a gallery that is not an embedded component of your store... if I spend too long in that gallery, the shopping cart section of the site will expire the session and the shopping cart will evaporate.
Customers will not (in the majority of cases) attempt to re-fill the cart and will simply take their business elsewhere.
So there are a LOT of supplementary technical AND procedural considerations - issues that relate to the protocols of things like cURL-based bi-directional communication, invoking of SSL at critical junctures, session management...
You only need to really concern yourself with the details of the above suff when you start looking for techniques to embed ZC into an established site. If you do the opposite (embed the site into ZC) then the above issues are largely taken care of.
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