I'll take a stab since I just installed a sub:
Usually, when installing an amp/sub, the only wire you would run to the battery is a large, red power cable that hooks up to only the POSITIVE side. In this case, my hunch is that that is the cut wire over the fuse box. That wire likely runs thru a hole in the firewall and powered the amp. Check under that black sheathing of the cut wire to see what color it is. In case you ever want to run a sub, you can leave the sheathed cut cable as is to use as a guide for your power cable to go thru the firewall. Or just reuse that one. From the inside of the car, you should see the cable(s) coming in near where the clutch pedal would normally enter the cabin.
Now as to what's happening on the negative terminal, more often you ground your amp/sub to a bolt somewhere INSIDE the car. There should be an existing ground bolt behind the rear, passenger-side seat. But in this case, they used the negative terminal on the engine battery instead. So the ground went negative terminal --> chassis using that Kicker adapter. I'm not sure about the 2011s, but if you look behind the rear seat on the frame of the car, you should be able to see where the factory wires are grounded (and where you should ground your amp if you decide to install one).
I'd remove the Kicker contraption, making sure you leave only the factory negative terminal hooked up and nothing else on that side. Then either leave or pull out that snipped, sheathed power cord from the inside of your car where the clutch pedal would be.
The first thing to do will be to unhook both the Kicker contraption as well as the car's power from the negative side. Once that is done, you can safely work on getting things back as close to stock as you want. You'll lose your settings after you hook the power back up.
Oh, and welcome to the forums!