Another Tuner question??

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I have a super chips racing tuner that I have been very happy with, but I am getting ready to do and EGR delete and the cruise won't work with this tuner if I do this. So I am leaning towards a hs xrt pro since I already have a edge cs monitor. Do I just have to return to stock and then plug to hs in or do I have to return to stock drive/start and then reprogram?? Two I have the exhaust with the bungs so sensors are plugged in Is this a problem with the hs?? Three what would be the best tunes to run I tow about 12k lbs quite often. Thanks in advance