Planets, stars, blackholes, etc will have gravity wells, and the FTL system will be sensitive to them, so the speed you can travel at superluminally will change based on the mass of the stellar objects around you.
Orbital mechanics will be simplified and be spline based. Dan recently posted that the ship will be free to fly where ever at sublight speeds up to a limit altitude around planets and such, at which point a shuttle would be needed to go further towards the surface.
A circular spline will be drawn around the planet that intersects with the ship. He said at the equator it would be horizontal and at the poles it would have a 90 degree inclination.
The physics state of the ship will be moved along the spline at a speed calculated to be what the ship would require to maintain that orbital altitude.
The result is that the ship will always be in a circular orbit, but you can change orbital altitude freely and the speed of the orbit will change accordingly.