One more comment, not from a techie point of view, just another person trying learn just-enough to get things to work properly. The 3 different web hosting companies I've used all made ssl fairly easy. Maybe there was such a folder as the one you speak of behind the scenes, but I sure never had to deal with it in this complicated way you mention. I only maintained the site in the public_html folder and made proper ssl settings in ViArt or my previous cart programs. I currently have a Thawte certificate, because that's who my hosting company uses. I am only paying $50/year since they buy certificates in bulk and pass along the savings. My hosting company fully set it up, I didn't have to struggle at all. another hosting company charged me $130/year.
The only tricky thing for me was when IE or Firefox would warn my customers my cart pages had both secure and unsecure content on the page. The problem went away when I changed a couple of my graphic callouts from http://site.com/images/graphic.jpg to
https://etc., or used a relative callout like //images/graphic.jpg
Wow, I think I'd give up if I had to manually put things in two different folders???!!! (maybe I am not understanding) Again, good luck!