When you export the shot from SynthEyes as a .ma, and import it into After Effects, it comes in as a composition with a bunch of 3d nulls representing tracking points, and a camera layer. When you drag your original footage into that composition as a 2d layer backplate, it should line up and you should see the nulls moving in sync with the background footage when you scrub the timeline. To place an image into the shot, you must make sure it is a 3d layer, (has the little 3d cube box checked) and that you are looking through the moving camera. If you saw the nulls moving when you scrubbed, then you are probably looking through that camera. If there is only one camera in the shot, you usually are looking through it, but you could be in front view or something. You can change cameras with the little dropdown tab at the bottom of the composition window.