I'm not at the machine at present, but track 1 is the skyline shot, track 2 is the title clip with a mask drawn around the sky of that same shot, and track 3 is a new clip with the sky material which is supposed to replace the content inside the mask.
The idea is to make the area enclosed with the mask transparent, and the area outside it, opaque. So I'd get the clouds from clip 3, but everything outside that mask would come from track 1.
Every combination of track matte filter I've tried (putting it on either track 1 or 2, and selecting the track above) seems to have no effect. The clip on track 3 is the only thing which appears.