I got a Bazooka amplified sub combo installed. I just bought a amp instilation kit from wal-mart and was mostly plug and play. Power wire off battery, ground screwed into body, remote wire spliced into AUX wire at back of HU, and RCA cables off back of HU.
When I had Sound Warehouse install my amp & sub, they couldn't get the amp to receive input from the head unit. They had to go into the "hidden" menu with the head unit power turned off & turn on the subwoofer. I have the basic head unit BTW.
Another thing, when I told them the stock head unit had RCA inputs built in, they didn't believe me. They said, "well, if it does have them, you'll save about $70 on installation, but we've never seen a factory stereo with them built in." Little did they know, I had watched a tutorial on our stereos on scionowners.com, & knew about the RCA inputs already.