2013 Chevy Malibu

You will have to run speaker wires all the way from the radio. Each speaker needs two wires. Buy speaker wire which is paired. Don't mix up polarity or the speakers will be out of phase.

How do I know where it goes if my car never came with them or could I merge them with the door speakers or something

You would have run the wires under the carpet. If your stereo does not have a rear channel this probably will not work.

Will I have to look at the back of my head unit to see that?

Obviously. Look for a wiring diagram which may be on the top.

I went to my local stereo install place and they hooked a little box to my radio and ran rca plugs to my amp for my 12s

I'm sure you can do the same for 6×9s