As part of the integration project for dashCommerce and Umbraco we decided to bundle the dashCommerce core functionality in a .Net Assembly (dashCommerce.Net.dll) rather than keep the project in it's current Web Site structure.  Principally this was done to simplify the integration with Umbraco.  In Umbraco the dashCommerce UI is implemented as .Net User Controls which reference the above assembly.  The user controls are rendered as Umbraco Macros within Umbraco Templates. 

Essentially I've replaced the .../App_Code/... and .../App_WebReferences/... folders with the .Net assembly (dashCommerce.Net.dll) . 

At present I've commented out the PayPal entries as updating the Web References is not working correctly in my VS project.  Also, I'm using a utility to create a proxy for the ASP.NET Profile that dashCommerce uses so I can work with it at design time.  Our design dictates that we'll use the Umbraco Members functionality in place of the ASP.Net Profile, but this is implemented as a provider with dashCommerce so I expect we'll have the option of either (depending on the state of the Profile Provider for Umbraco next week).

I used a post from Scott Guthrie to get started on this but took a slightly different approach.  Rather than suck over the entire web site into a new Web Application project I created a new C# Class project and just worked with the .../App_Code/... folder as well as adding in the required references.  Once this compiled successfully I simply referenced the new assembly in my Umbraco User Control Project (aka, the Commerce.* namespace).