Hi Katie, welcome to genvibe.I think the second plug has only one wire, or perhaps only one wire used, and it's suppsoedly a mute control for the amp on Vibes with the Moon&Tunes, (or sun and sound) package. I don't know it if really does anything anyway, I replaced the radio in a Matrix that had the sunroof and under seat amp, and it had no second connector for the radio.
http://forums.genvibe.com/zerothread?id=6799 has some various discussions about pinouts, the viberadio.gif linked there is also useful