You store the stock file on your laptop or remote tune device depending on what tuner & version you go with. They will send you the device or cable to hook up to your laptop. You e-mail the tuner your stock file & tell them what you have on your car, pulley, HFC's, & what gas you run. You also tell them to increase the RPM, delimit the speedo & remove cat warm up cycle if you want. They e-mail you back the tune & you load it. Done.
You can flash it back to stock anytime you want. It's pretty simple.