If your tracking gives you less than satisfactory results, give some of these options a try. While they'll take longer to process, you may get better results.
You may want to track position and rotation, which will give you two tracking regions positioned diagonally. If the footage is interlaced, try tracking fields. If the shot has a lot of movement, try going to the final frame and tracking in reverse.
Try modifying the options by clicking the Options Button above the play button in the tracker controls palette. In AE 6.0, you need to click Options again near the tracker plug-in selector.
In AE 6.5, the tracker window is simplified and you only need to click Options once.
You can choose to track the RGB, Luminance, or Saturation Channels of a region.
Try enhancing your footage by temporarily blurring or sharpening it. (The blur or sharpen is only for tracking and not actually applied to the layer).
You can track using subpixel positioning where the tracker analyzes position between pixels, and you can tell After Effects to guess at the closest position with the Extrapolate Motion if Confidence is Below _%. The extrapolate option is handy for when your tracking feature becomes temporarily hidden.