In SWX simulation I've never seen any way to directly interact with the mesh to locate loads & constraints.
If I understand your problem correctly, the method I would use would be to use split faces. This can be done by creating a plane roughly parallel to the top face of the I-beam and sketching the locations of the rafters & supports on that plane. Then split the top face (or other location if req'd, e.g., if the supports go to the bottom of the beam) by selecting Features/Curves/Split Line and projecting your sketch onto the appropriate surface. These faces can be selected to apply loads or constraints. You may have to get creative to apply the loads in whatever direction you feel is most correct in the area where the beam is twisted the most.
If that beam is as big as it measures in SWX, I am wondering how you were able to scan it?
In this screenshot I offset the sketch plane just for clarity. Hope this helps.