We currently use BH but not with Align RT. At Sim, we mark our fiducial in FB and scan. When we do the BH scan, we put the patient in BH and move the table back to the fiducial we marked in FB, and scan. In the treatment room, set the patient up to the FB marks. Put the patient in BH and move table out/in to get back on the tattoo/mark. Let the patient breathe and do the shifts. You should now be at the proper shifts for BH. We only use the BH sim scan for planning as well.
Not sure if this is what you were looking for!