I bought a stereo for my 2006 scion tc but I am having issues with getting it put in. The stock radio has about 3 different harnesses plugged in and I dont know which one to use? Some of the colors are missing on each of them also such as red and black/battery and ingnition?

 

You have to get a aftermarket wiring harness for it. Just go to best buy and tell them what car you have and they will hook you up.

 

The car should use the Metra 70-1761 harness, which Best Buy sells. You'll probably need a fit kit / dash kit / trim kit for the car depending on what size radio you are using.
IF you want to keep your steering wheel controls AND your aftermarket radio SUPPORTS a wired remote/steering wheel controls, pick up a steering wheel control interface that works with the brand of radio that you plan on putting in, they might be universal at this point but depends on the radio.
Also, I believe the 06 started the AUX and IPOD input in the center glove box, you'll lose those with the aftermarket radio but depending on what radio you plan on putting it, it should have it's own AUX and IPOD functions.