C#.net 2008 build issue

I have the following question to ask about compiling a C#.net 2008 web and desktop application:
I would like to know how to properly change the configuration manager. To get this application to run initially, I opened the XML file called 'App1.allusers.exe.config' and made the appropriate changes while the application is executing in debug mode. As you can see, the file I am referring to was obtained from the C#.net remoting setup. See the code listed below:
 RemotingConfiguration.Configure("App1.allusers.exe.config", false);
 I made this change just to get this application to run.
However, can you tell me how to make the changes in the configuration manager for debug mode so that the changes are saved in the correctly and the values go to the App1.allusers.exe.config file when I want to run a  build?