Does it support USB? Cause I wouldn't want to get anything that takes up my PS2 ports. Those I want restricted to my original Keyboard and mouse.
As for your question, it shouldn't matter which one is ground or positive. Ground is usually shared among all the other ground connections. They just did the work for you of adding the ground as a pair for each wire. Unless your panel is on metal, which I doubt, ground shouldn't really matter. Even if it was on metal since it doesn't come in contact with the metal CP.
Just think of it as a switch. Touch the two contacts together and it triggers the button or joystick press regardless of which one is ground or positive. So you can connect them either way. Just keep them away from all the other contacts. You wouldn't want to short something out and break your nifty little contraption. Not that I know anything about it. I'd rather go for the I-Pac.