You have a misunderstanding of how RT platforms are intended to be used. Don't worry, you're not the first one, and there will be more that come along after you. They should run stand alone and are not intended to have a user interface. You should have an application on your PC that handles all the user interface stuff and communicates with the cRIO via some type of network communication. The user should never be setting control values directly on the cRIO; the ability to do this is purely for development and debugging purposes.
What I have done in the past for configuration files is, modify the configuration file on the host and when it is saved, FTP the file down to your RT platform (cRIO). You can do this in your program by having a dialog that allows editing of all config file parameters, and has a save button. When save is pressed, use the FTP VIs to FTP the file.
On the cRIO you have a loop that is monitoring a directory. When it sees the file in the directory is new, it reads the file and updates the values in your RT program. Does this make sense?
