How do I remove wordpress them & replace with custom

I’ve designed and coded a complete site using HTML, Flash & CSS and would like to use wordpress to run the e-commerce & blog portion of my site. What is the best way to integrate this? I’ve downloaded wordpress to my server, http://www.domainname.com in the main directory.

My preference would be to continue to edit the HTML & CSS outside of wordpress, is this possible?

Where do I go from here.

thanks
Josh