Don't worry -- a help file is on the "todo" list. But for now...
Run the application. On first run, you will need to select "RadioShack Scanner Control Protocol Scanners by GRE", the top choice, and click Properties. Select Pro-79 from the list of scanners, and click OK. Then click OK on the Modules dialog.
Begin entering frequencies by double clicking the corresponding box, much like you would in Excel or other spreadsheet programs. Do not forget to save periodically. When you are satisfied, connect the programming cable to the COM port specified in the Module Properties (I believe it defaults to COM1). The USB cable also reportedly works.
Turn your scanner off. Hold down 9 and ENT while turning it on. The screen will say "WIRED". Select Options -> Upload All To Scanner (or select the ones you want to upload and click Upload Selected). It will go through the frequencies, and programming all 200 takes only a couple seconds. When it is done it will say "End". Turn the scanner off, unplug the programming cable, and turn it back on.
If you have any questions please feel free to ask -- I have a Pro-79 too -- and I wrote the software.