It appears that we are unable to create folders within the C# template project. What it appears is happening is that SQL Packager takes a copy of the top-level C# template folder only. At compile-time this means that any classes defined in sub folders are missing.
For example, I can add a class file to to the project at the root level, and it compiles fine. If I then simply move that class file into a project folder, the project will compile fine in Visual Studio, but fail to compile in SQL Packager. The compiler complains that it cannot locate the class.
This is an organizational inconvenience only. I can make the template work, but I'd rather adhere to our coding standards and structure the project accordingly.