Vince is exactly correct. The .mxf file is the one that has your complete setup. A .mxd file is specific to a single device (although it can contain multiple devices - my 990 file has a 990 device, a tuner device, and a zone2 device) and can be imported into a .mxf file. You'll need to right-click on a device under "Home" on the left side of the screen and choose "Import Device" to bring the configuration file into your file.