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Well, you use MakerWare / Desktop if this will be the first time Sailfish is installed on the printer. I have no idea what firmware CTC initially installed on your printer. If it was MBI's 7.x firmware, then you should do that step so as to preserve your X and Y toolhead offsets (assuming they've been calibrated). If the original firmware was Sailfish of some flavor, then you don't need to do that. And, of course, you can always re-calibrate the toolhead offsets if/when you want to do a dual extrusion print.