If you are working with the mojoPortal source code I recommend study the post build events for WebStore and/or mojoPortal.Features.UI to get the idea how it works and notice how the features are organized into folders within their projects, ie the WebStore feature has all its pages and user controls in the /WebStore folder within the project and that needs to land at "$(SolutionDir)Web\WebStore\"
Hope that helps,
Joe