Is it possible to set more than one motion tracking point in After Affects CS6 at the same time
Sounds like you need to track the camera in 3D. If you're using CS6 then the best thing for tracking the camera in 3D is the 3D camera tracker (who'da thunk it).

To fire it up Choose Animation &gt; Track Camera, or choose Track Camera from the layer context menu, or choose Effect &gt; Perspective &gt; 3D Camera Tracker, or (because there's always 3 ways to do anything in AE) in the Tracker panel, click the Track Camera button.

After tracking the camera in you footage you have a virtual stage, where any 3D objects that you add will look as though they're in the 3D space of your footage, so if you move past them they respect the parallax of your camera's viewport. It makes it super easy to add elements to a moving camera scene.

Here be tutorial and the Adobe page about it.

Oh and to actually answer your question, yes you can have more than one track point per layer. For 2D tracking where I'm not getting steady results I often make a dozen or so track points and average out their position with an expression. This gives good results on difficult footage. To add track points, select the layer, choose Animation&gt;Track Motion. Set the track type to Raw in the tracker panel. Then in the timeline you'll see the Motion Trackers property has been added to the layer. Expand that and you'll see tracker1, expand that and you'll see Track Point 1.



Select that and choose Edit&gt;Duplicate or hit cmd/ctrl+D. The track point will be duplicated. Note that it will be right on top of the other one, so you'll have to move it in the comp window or adjust the feature centre properties. Repeat as many times as you need.

Now when you go to Analyze using the tracker panel it will analyze all your track points at once.

Oh and FYI here's the expression I use when I'm adding all the track points together. I apply it to the position of a null or whatever it is I want to move:

trackpoints=10;    
vsum=[0,0];
for (i=1; i&lt;=trackpoints; i++){
    vsum+=thisComp.layer("tracked layer name").motionTracker("Tracker 1")("Track Point "+i).featureCenter
}
vsum/trackpoints


trackpoints is the number of track points you're using. and "tracked layer name" is the layer with the points on it.