PMDG & FS Commander 8.1

My question is about linking the AP to external navigation tools. I have been using FS Commander for a while and use it extensavely for its information & navigational ease. It does export to a PMDG format but I find as it is faily up to date it causes errors in loading files because the PMDG database might not know a waypoint.I run FS Commander on another machine using FSUIPC and it is great for visual referance on your navigation. Due to flying online it also gives great representation of other aircraft. I was wondering if it can be coupled to the autopilit heading in the 747 Queen of the skys to control the autopilot as it doeas with all other aircraft I use in FS9.I understand your target market is the actual realism of your simulator, and that is the exact reason I purchased it, but if we could navigate using a 3rd party GPS tool like FS Commander that would be great.Can anyone please advise if this can be done.