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When you solve a scene with motion capture trackers, each of them will have a 3D key frame on every frame of the shot, animating the tracker's path. The result is an animated point cloud.
Generally you will want to be able to apply the motion capture data to a rig in your 3D animation package, to make the matching rig move the same way. The rig's dimensions may match the original character being tracked, or be different. You can do that using SynthEyes, or your animation package.
Using SynthEyes, you create a rig and cause it to match the motion of your motion capture trackers. Those are done using the Geometric Hierarchy features of SynthEyes. Then, you export using the "Biovision" BVH format, which is a good way to communicate rig animation between packages, as it contains only the joint angles of the character. Finally, in your animation package, you can import the BVH data to your character. See the Geometric Hierarchy Tracking manual for more information, see the section "GeoH Track with 3D Motion Capture Trackers."
Using your animation package, it is up to you to determine a method of rigging your character to take advantage of the animated tracker paths. The method chosen will depend on your character and animation software package. It is likely you will need some expressions (formulas) and some Look-At controls. For full-body motion capture, you will need to take into account the offsets from the tracking markers (ie balls) to the actual joint locations.
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