2009 Scion tC

Without reading up on the stock wiring harness for the TC's, I can tell you that YES, you can always add subwoofers/amplifiers without having to tap into your stock head unit.

There is a neat little $15 dollar device called a 'Line Out Converter' which takes the regular audio signal that is sent to your speakers, and converts it into two RCA jacks, which are required for your amplifier. You can get this device at Wal-mart for cheap, and at almost any stereo shop.

Now, i'll check around a little later today, but i'm pretty sure the new TC's have some preemptive pre-outs (they put them in place so you wouldn't have to change out the stock headunit) and in that case you'll be in luck!