Did this, this past Friday. Second time changing the main battery because of the aux battery, which I feel is the only reason the main battery dies sooner than it should. Disconnected the negative cable and pulled fuse 42, no issues since then. I have had the smart startstop bypass for a few...
Have you had any issues starting your jeep? I believe that's an indicator the small battery for the start/stop function is going to be gone soon. And it takes the main battery with it. I just replaced my main battery yesterday. I got the the "aux switches not available battery charging" message...
Can you tell what brand it is? The only 2 underseat lockbox options I remember from jku were bestop or tuffy security. Maybe email and see if they can get you a replacement key.
I think you'll be pleasantly surprised. I have the dart speakers in dash and soundbar, and went with a kenwood ksc-sw11 powered sub. I'm in a 2 door so I didn't need a ton of bass, the sub sits right behind the passenger seat. Big improvement over stock.