We use AlignRT on all our breast patients and have found the system extremely useful for large pendulous breasts. We do treat on a breastboard, normally on an incline of about 12.5, and this does help the breast to fall inf as well as laterally. I would go ahead and draw your ROI to cover the entirety of the breast tissue, and see how you go on fraction 1. You can always amend your ROI with the patient on the bed too to include more or less. Perhaps just allow her an extra 5mins on Day 1. If you want me to have a look at the ROI you draw just post it on here, without any identifiable patient data on there.
Let me know how you get on