Sorry to be thick but which DNN Templates? I have the Module entirely inside its own folder on the DeskTopModules folder of the website within a VS2008 Project. I did a Publish Web Site and fished out the dlls for the Module in question.

When you are creating a dotnetnuke module (yes using the starter kit)  you can create the modules inside a website (which seems to be the aproach your using) or create them as another project which can be part of the global solution. When you create them as part of the website the files are created inside the deskotp modules but there's no way to generate an encapsulating dll for all the module's code (at least I've tried without succeding)

So when you want to use the module you use the "import manifest file" from the module extension module and then you pack it

But when you create it as another project inside the main solution you can actually create an encapsulation dll which you later copy to the binaries folder, create a folder for your module on the Desktop Module and copy al the files (js/css,ascx, ashx, and so on even the bin files) to the folder (except the source code and the debug files) then you can use the import manifest feature and finally you can procced to pack it