If Yamaha has new setup software, you would plug your computer's 9-pin serial port into the receiver's 9-pin serial port (RS-232) and use the software to configure your reciver. This is, obviously, something you have already done manually, so it isn't necessary.
If your receiver is 100% setup the way you like it, then with the software you could connect to the receiver, and save the receiver's current settings to your PC. That way, if you have a service issue, or someone messes everything up, you can load it from your PC.
Unfortunately, I am not aware of new software being available that controls the 2500 - at least it isn't on Yamaha's main website. I know I have the program for my Z1 and it is pretty cool.
I use the port for control of my Z1 with a Crestron control system. The port allows for full discrete power on/off, source selection, and volume control for all zones. Good stuff when the receiver is 50 feet away from the room you are sitting in.