[arduino DUE] use programming usb port with native usb port?

Reading the arduino due tutorial, i've see that native usb port coulb be used for load arduino sketch too (but it's not recomended). Now i would know what it means that it's not recomemended. I would write a sketch that read data from some sensors, then write a file reading by an application on my pc that compute the result. The firs solution could be load sketck by programming port, then connect arduino with native port and let it run. But is so frustrating to to that in phase of develop (plug and unplug usb from port to another). How can i do that? can i use simply the native usb without problems for load sketch, or i should buy another usb cable to connect it ?