Hi. Autopilot MFD is now severely outdated. The surface base structure has some significant changes inside the 2006 release. If you want to use it, you will have to make the changes yourself. I suggest you look at the default file structure and read the orbiter manual in order to find how surface bases work in Orbiter.
You will basically need to move all the base configuration files that come with the MFD inside /orbiter/config/Earth/Base folder. Then you will need to manually edit each configuration file to
reflect the changes inside the 2006 release. Make sure you don't overwrite the Earth.cfg with the one that comes with the MFD, as it will most likely cause a CTD because of the changes made in 2006 release.