no. you choose one signal, then it will create one single calib.csv only, and then you'll use it for any other type of signal later on (by loading it from app path/calib.csv). i suggest you use sine during calibration since its mostly used, i only provide flexibility, say if you want to work mostly on square, then you may want to calibrate using square signal. but if you look carefully, the method is not so perfect, esp at high frequency. if you want different signal with different calibration file, then you should save each files yourself. to load it, rename to calib.csv and put in application folder, open the application and it will be loaded.
about the auto/manual button. AUTO will calibrate your device at predefined frequency set in
auto.csv in app folder. MANUAL will calibrate your device based on frequency (min, max, step) that you put in application textboxes (the same textboxes to be used as sweep function).
reconstruct button... say if you did manual calibration at frequency 100-1000Hz, and later on decided to calibrate at 1000-1,000,000 Hz, the older (100-1000Hz) calib.csv will be overwritten, but not the raw files (many files you can check in My Hantek Files\Calibration). now you got new calib.csv for 1000-1MHz only, to combine all the 100-1000 and 1000-1MHz raw files into one single calib.csv, then you should press reconstruct button, when its finish, you'll got a calib.csv for 100-1MHz.
sorry its not very clear, i was lazy to type a dedicated help file for that particular function. there only a few of us here, so i guess they can read it here as well, so i guess my part of explaining it is done in this post