I'm not sure I understand what you mean by the 'prong' next to JP3. The two header pins sticking out sideways are
JP3. You fit the little black jumper header onto them in order to provide power to the 6-pin and 10-pin headers.
The jumper header should be removed if the target board has its own power.
does talk about it:
Jumper JP3 (USB power to target)
There's a jumper sticking out near the cables, JP3. When the jumper is in place (connecting the two wires) then that means that the USBtinyISP is providing 5V power to the device being programmed. If you don't want to power the device then just take the jumper out or make sure its only on one of the wires.
BTW, some of your parts look a little unusual. Where did you purchase this kit?