Aftermarket speaker subs installation?

Most of the time the sub-woofer speaker with come with instruction's but if you don't have them you will need to supply fuse power (on with the key) and ground to the sub woofer speaker and then tap into the subwoofer wiring the car already has, here are the wiring colors in the images below so you know which wires to connect. If you have problems, please upload images or a short video so I can help walk you through the job. Check out the images (below). Let us know if you need anything else.

The OE amp likely won't be able to drive both of them, however you could use the OE subwoofer outputs to drive a different amplifier to handle the 2 subwoofers. You would connect them up in parallel and then to the subwoofer amp. For the amp you would use a mono (single channel) amplifier with speaker level inputs. Like a Kicker CX 400 watt or a Kenwood KAC-511. Just be sure to run a good set of power cables to the amp. Don't try to power it off any of the stock wiring.
As for an aftermarket deck, you are correct however it isn't just the heater controls that run through that stock unit. There are multiple other modules that also get information through it. The high level of integration is why you don't see a lot of aftermarket units these days. Some vehicles are even worse, the display units on them are nothing but a computer screen and all the other parts are scattered around the vehicle. Yours only has the parts shown in the image that are the "radio".