To get started, open Mannequin and select "Load Preview Setup" for the character you want to edit. For example: Animations/Mannequin/Preview/SDK_playerPreview1P.xml
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If your fragment is called "<default>", it will be played whenever a system requests a fragment for the ID. You might not always want this: sometimes, for example, the animation is authored for "relaxed" stance with a "rifle" weapontype. To mark the fragment for this specific context, select the appropriate tags.
In this example, select Stance="Relaxed" and WeaponType="Rifle" in the list of tags in the bottom left. The fragment should now be named "rifle+relaxed". Note that if a system now selects your ID and no fragment is available for the current context (say the AI is Alerted instead of Relaxed), NOTHING will happen.
For smart object that need precise alignment, you need to add a PositionAdjust procedural clip.
File/Save Changes...
There should be 3 files:
Animations/Mannequin/ADB/XXX.adb
Animations/Mannequin/ADB/XXXControllerDefs.xml
Animations/Mannequin/ADB/XXXActions.xml
Check out files if you need to.
Press save and you're done!