I believe the DNN document tells you how to setup in Visual Studio. I will tell what I am doing, but I am not sure that it conforms to best practice as I have not read anything on the subject in some time. I migrated my project from Visual Studio and had to use both VWD 2005 Express and VB 2005 Express. Here's what I've got setup:
VWD 2005 Express
Simply a web project over the DotNetNuke folder and is only used for debugging.
VB 2005 Express
A solution with two projects:
1. My Project
a. The files are in DotNetNuke/DesktopModules/MyProject
b. This project references Dotnetnuke, Dotnetnuke.webutility, system.web, etc.
c. Builds to it's own \bin
2. _BuildSupport
a. This project references My Project
b. The output for this project is set to go to DotNetNuke\Bin
It is a bit of a pain, but it works. Maybe someone else out there can make a better recommendation or reference documentation.