i'm not sure i understand. Are you talking about manual or automatic tracking points? so you have them selected and you can't unselect them? I just left clicked and they deselect.

i've only just tried matchmover, but You will find most matchmove programs are the same really.

matchmover:
1. load the sequence
2. check/change your camera settings
3. click 2d tracking> automatic tracking.
3b. uncheck solve camera.
3c. click settings and change the sensitivity and density.
3d. click ok
4. clean up the auto
5. solve camera
6 check focal length
7. export to maya
8. group everything and rotate/scale/translate the group to align the scene.

i think this is pretty much it.