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.

Is my car going to be able to handle 2 12" JL Audio subs?

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".

So, I got the box and the wiring and now I'm lost at how to hook it up in my car, literally never done this before. Would I need a power cap too or not?

Where's the wiring for the factory sub? And is there a factory amp then too?

The factory amp is in the trunk. You could use the output from it to drive the aftermarket amp. This is the wiring it uses. You shouldn't need any caps, but they don't hurt. You need to run the power to the amp and then use the factory sub connection from the oe amp as the signal. There are a few videos out there if you want to look at them to get an idea of how to wire it.

Okay, so I bought this today so needing to know how to hook it up to the factory sub and radio.

Like if I were to keep my factory sub and amp like you said where would I hook that up to this thing at?

That is a line level converter. It would get connected to the sub connection in the schematic I posted. It would connect to the light blue and gray wires. Then it's output would go to the new amp and those connect to the subwoofers. Your connections will be to the amplifier, not to the radio.

Don't understand anything you're saying. I give up.

You go to the subwoofer in your car that is already there. That gets disconnected from the amplifier that is already there. Those are the Gray and Light Blue wires. Now the two wires that went to that subwoofer get connected the line level unit you bought. Then the output of that unit connects to the new amp and the subwoofers that you have. No way to explain it any easier.