I believe if you have a boned model you can manipulate the bones directly from within B3D. So you will need to orient the bones to match the angles of the limbs of your ragdoll.
Presumably your ragdoll has a vertex at each joint position? If so, you can work out the orientation that would be required for a limb positioned at (for example) the shoulder vertex to point towards the elbow vertex. Repeat this for all limbs and the boned model should follow your ragdoll's shape.
Presumably your ragdoll has a vertex at each joint position? If so, you can work out the orientation that would be required for a limb positioned at (for example) the shoulder vertex to point towards the elbow vertex. Repeat this for all limbs and the boned model should follow your ragdoll's shape.