You can only tint over the 3rd brake light if you have a spoiler with a built in brake light (like OEM). Otherwise, you are breaking the law and risk getting hit from behind. If you get hit, most likely you will have to pay, even if it wasn't your fault, because your light was covered and the other party could claim "I didn't know he was stopping".
Enough of that. You need to remove the entire subwoofer cover. First open the trunk and make sure that the 3rd brake light is completely unhooked. I had the spoiler installed, but they only had to unplug half of the light behind the window to plug into the spoiler, so the other half was still plugged in.
The subwoofer cover is not screwed on or anything. Just get a flat screwdriver and carefully (so you don't ruin the plastic) pry it up and it should pop out. You should have access to the entire window now.