PDshop handles the switch between the SSL and your regular URL automatically, all you do is enter the correct URLs in PDadmin.  For example, when the checkout process begins the browser will be redirected to the SSL url, and when the sale is completed, they will be sent back to regular url.

As for placement of files (if you are using a shared SSL), simply copy all of them to both directories (the regular and the secure folder), so you'll have two copies of the store running.  The only difference between the two is the setup.asp file which may need to be different depending on your db connection.  The only other issue (or drawback to using a shared SSL) is with images, you may need to place a copy of some uploaded images in the secure folder as well (not all images, just ones that will appear on the top/bottom sections of the storefront, and the checkout help pages... Item images only need to be in the regular images folder)