Well, provided you know what you are doing, then once you have set up Zen Cart (in a folder as you mentioned) you can copy the Add To Cart links for products into your main (HTML?) website.

But this creates problems of PHP sessions being lost if people backtrack from the Zen Cart site to the main website.

Overall the best approach is to install Zen Cart in a folder, make it look as much like your main website as you can, then remove your main website and move the Zen Cart site out of the folder and into the root (replacing your old website).

Vger