When you are debugging a code nanite this is how you setup your environment. (1) Specify the path to your CodeStencil executable. It will usually be under Program File (x86), in the Zera Systems folder: "C:\Program Files (x86)\Zera Systems\CodeStencil ...
The file - CodeStencil.Debug.xml lets you specify where your code nanites are loaded from. This can become quite useful when you are trying to step through the code you have written for a code nanite. This is what the file looks like: <?xml ...
One way to validate/confirm where your assemblies are loaded from is from the "About" menu. This window displays a list of the assemblies that have been loaded and where they were loaded from.