moving DNN installation from root to subdirectory

I have installed Dot Net Nuke to root directory but want to run other applications in a subdirectory. I get this error from subdirectory:

Server Error in '/****.com' Application.
Line 99: -->
Line 100: <codeSubDirectories>
Line 101: <add directoryName="HTML" />

I assume this is due to the DNN code in \htdocs\web.config

Is there an easy way to either move my DNN configuration to a subdirectory (but it already has a few portals on it), or (preferably) to prevent the subdirectory application from referring to DNN's root web.config.

Eternal gratitude if you can help!