Yann, at GPS-AR has a forum he answers questions on.
gpsactionreplay.free.fr/forum/viewforum.php?f=10&sid=fb9019663a13fc0bdc7920b44dd9aab1GPSAR was originally set up for gpx. Can you download from the Navi directly in gpx?
When Doppler started being used ,Yann after offering gpsar for free for about 3 years decided to keep the new functions for an improved version he called gpsarPro which he charges a small fee for. I think on this version you can directly upload doppler results.
There is also a program called GpsResults with a free trial period you can try. It's quite nice.
www.gps-speed.com/