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To use it, you connect it to its power supply and to a dedicated piece of track which you'll use for a programming track. Also, connect the 25 pin RS232 connector to a serial port on your computer. You may have to use a USB to serial adapter, and/or a DB25 to DB9 connector adapter (The PR2 has a standard RS232 25 pin connector; most computers now have a 9 pin RS232 connector, and there are simple adapters available to convert the wiring.)
The PR2 is not a LocoNet® interface, and does not connect to the LocoNet on your layout in any way. It cannot attach to a command station like the MS100, PR3, LocoBuffer, LocoBuffer-II, and LocoBuffer-USB do. The cable that comes with the PR2 is not a LocoNet cable, and you should not plug a LocoNet cable into the PR2.
To set up DecoderPro to use the PR2:
You can use a JMRI throttle to control the locomotive connected to the PR2. Use the JMRI Power Control or the "Power" menu item on the Throttle's menu bar to turn on track power, and then you can operate the locomotive normally.
The PR2 can only provide very limited current, so Digitrax has built a "neutral mode" into their sound decoders. When JMRI and the PR2 is running a Digitrax sound decoder, the motor is disconnected to reduce the current load. You can still ramp the speed up and down with the throttle and listen to how the sound responds, but the motor won't move the locomotive.
Other decoders, including decoders from other manufacturers, may draw enough motor current to trip the PR2 internal circuit breakers. This will cause JMRI to mark track power as "off". Just wait a couple seconds and turn the track power back on to recover.
LocoNet® is a registered trademark of Digitrax, Inc.