I know in Mocha AE you can tell it to auto track and you can also create manual keyframes. For areas that it could not auto-track I created a handful of keyframes and of course those parts of the timeline are now red rather than blue. When I create tracking data in AE the durations where the timeline in mocha is red the tracking in AE stays still even though the spline matches well in mocha.
red is what it has not tracked. if you change the mask at any time, mocha will try to auto compensate to match so just let it track everything then go in anc change and retrack if needed. also make sure your layer duration does not extend the area you want to track