YES. You can make changes to the HTML, CSS, and ASP.NET code to further enhance your online storefront.  

For HTML (design/look) changes, you would simply modify the "template.htm" and "template.css" files. PDshop has a built in HTML/CSS template system, which makes design changes very, very easy.   You can also modify the template.master file (PDshop now supports Asp.Net master pages).

For functionality changes, you would simply modify the ".aspx" files, the template.master, or the ".vb" file).