Web projects in Visual Studio 2010 have the ability to define web.config transformations. That way a developer can create web.config files for each solution configuration based on a base web.config. Sadly this functionality is only available for web.config files. Other configuration files, like the aap.config, are not supported. So it seems anyway. The following links show how to make it work for every config file.
I hope this information will help you with your projects. Happy programming.