Craig, you are correct under portal development mode. Even if you use ASPX Pages a lot of the information is stored within the database.
What I do is use the Kentico Installation Manager KIM. That will create me a blank site with all the templates that I need.
If you are talking about modifying or your site with all of your customizations that is easy. You would just create a blank site with KIM then just export your existing site or the site you will create, and import into the new site.
For example. I have a standard tree, options, settings and multiple page designs that I use as a base. I have exported it from the site. Everytime I set up a new site, I just install a blank portal site and import my exported package.