This seems to be done automatically in a limited regard. It would be nice to have control over whether we're seeing our velocity (and prograde/retrograde markers) relative to the rotating ground, non-rotating orbit, or even our target--especially when rendezvousing and docking in the latter case.
You can click on the SURFACE text above the velocity to switch to ORBIT and then if you have a current target TARGET mode. When you are in TARGET mode, the velocity prograde and retrograde indicators are relative to the (target.velocity - player.velocity) vector.