A good reference point is a high-contrast pattern that has good definition both vertically and horizontally.
Selecting a good reference point is a process of trial and error. Play the clip several times to become familiar with the material. Ideally, you should try to find a pattern that is present in every frame. In some cases, this is not always possible and you may have to track two different patterns, track an object that disappears behind another one, or track an object that moves out of the frame. For more information, see Tracking Difficult Shots and Correcting Errors.
The frame you use for the reference point should be the frame where the reference image is most representative in terms of shape, size, and rotation. You can select the reference point from a frame in the middle of the sequence, if the pattern you want to use as a reference is subject to a lot of rotation or scaling. In most cases, you will position the reference box over the reference point in the first frame of the sequence.