I presume your question is about the initial set up for free breathing patient with or without tattoo. In other word you would like to know what to use for the patient set up on the treatment couch at the first fraction and what to use for the subsequent ones. Is it the body structure set generated and exported from the TPS OR the reference surface that can be captured by the Align-RT camera? I hope I have got this right!
In fact the body structure set will have to be utilized as the first aid to setup the patient followed by the kV/MV/CBCT imaging alignment. The Body contouring alignment gets the patient very close to the right treatment position, which is verified or corrected within the imaging process. As soon as this step is completed, a reference surface can be captured and then utilized for the rest of the treatment course, while a reduced frequent imaging regimen is applied to regularly validate the reference surface. The reference surface may be changed during the treatment course if the imaging process suggests so.
I hope this helps.