The route in Mapsourse do not equal route in navi on big distance usualy. If you try time by time to adapt settings for routing in Mapsourse and navi may be you will have the equal routes. It is so difficult, trust me.
If you want drive by usual main roads network simply put key waipont from Mapsourse to navi and build route. No problem in unknown places!
If you want modify route by only selected route path you need edit route in navi by hot situation on screen map only.