Your GPS should give you a figure of merit or accuracy - usually accuracy for civilian models. You are someplace within a sphere defined by that radius, whether you are on the ground or airborne.
Your greatest accuracy requires 3D, which in turn requires a minimum of 4 satellites, the more satellites you get, theoretically the more accurate your fix should be.
Now, if you are talking about marking waypoints from the air, the accuracy of those waypoints will depend on the accuracy of the GPS, how fast the aircraft the is moving, how fast you push the button and how fast the GPS reads the position and you push the button.
Your point could be off by a few hundred feet, but in most cases, it won't matter.
Now, if you're planning on navigating to a waypoint in the dark and there are cliffs around, I would advise against it

.