I've got some footage of a city flyover where the camera is moving fast toward a city, and then flies through the buildings. I have to make it look like the city's on fire with explosions everywhere. These, naturally, have to match the motion of the flyover.
Is there a way to do this by selecting a start and end point and telling motion to match that point rather than having to painstakingly do it visually frame by frame? It couldn't be a linear 'start to finish' line as it would have to match the "building's" location in each frame, which isn't a straight line
That's called "tracking" and "match-moving". Motion has a pretty good tracker, but it's a bit complicated to use. You'll apply the tracker and the match-move as behaviors. I'd recommend looking up tracking & match-moving in the manual and keep it open as a reference while you work.
It might help you to think about it like this: make the city its own group, and inside that group, you can layer 2-d fire footage, explosion footage,and particle emitter effects where they need to be.
Once all that is in one master group "container", it becomes easier to fly the camera around using a few keyframes and bezier ease-in/out curves. By moving the group and the camera independently, you get much of the effect of a real 3- composition, even if you mostly use 2-d elements in a 3-d space.