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This feature requires some extra setup when exporting your agent type config.

You will need both your skeleton and animation controls in your scene, ; they can be part of the same rig or coming from two different rigs. 

You map joints to controls within the "Setup" tab of the Animation Rig Retarget Tool. 

Every time you select a joint, the tool will cache it, leaving you free to select any other item in the scene. Select the controls you want to map to the current joint and click on the "Add button".

If you are not happy with the mapping list for a joint, you can remove an item at any point by selecting it from the list and pressing the "Remove" button.

If you don't want the joint selection to be automatic, you can toggle the "Automatic selection" checkbox.

Once your control mapping is done, export your agent type config.

The retargeting tool needs an FBX file as input. You can export an FBX file from your agent group simulation with the Atoms FBX exporter (Atoms > Exporters > FBX Exporter).

In your animation scene, import/reference your animation rig.
From the "Retargeting" tab provide the namespace you used when importing your rig (optional) and the FBX you previously exported. 

Click on "Run".

The retargeting process will match your rig with the FBX animation.

Key frames Keyframes on the animation controls will be created following the key frames keyframes of the FBX joints. For this reason, if the FBX animation is not baked, you'll see key frames keyframes on the controls only on certain frames.
The tangent types are also copied from the FBX key frames to the animation controls.