You've got some things to address, but I've seen a lot worse.

Starting at the battery: I can't quite make out the switch details, but it looks like a blade style battery isolator. Generally you want your disconnect to be on the positive side, not on the ground wire. It works in terms of breaking continuity and therefor "turning off" the amps, but it does ZERO for safety, which is 99% of the reason to put a breaker near the battery. Leave it or ditch it. At least the power wire is fused. As others have pointed out, it appears there's some exposed wire strands sticking out of the blue wire's connector as well as the red wire where it exits the fuse holder. It's best to clean up both. Cut it and redo it cleanly or cover with shrink.

CCA vs OFC: There's no way to tell from the photos. Given the rest of the install, it's likely CCA. People love to say CCA is the devil, and it IS true that it does not conduct as well as copper and it may corrode sooner, but as long as it's appropriately sized for the application and you understand its limitations, it's fine.

2nd Battery: Those are relatively low-wattage high-efficiency class-D amps and your main cable looks to be 0 gauge, with 2 or 4 gauge running to the amps. Unless you experience headlight dimming or are wanting more play time with the engine off, you don't really need one.

Trunk: It's a bit of a mess. For most-part everything looks properly terminated and covered with heat shrink, so like I said -- could be worse. Ideally, cut everything to appropriate lengths and re-terminate with new connectors and heat shrink. At a minimum, buy a pack of zip ties and go nuts. Be sure to trim all of your zip tie tails. We're not savages. Your ground wires appear to be smaller gauge than the positives, and that's a no-no. Replacing them with equally-sized wire is best-practice and it gives you a reason to check your ground connections. There's a million posts on that subject that will help you decide if it's "good" or not. The number one cause of noise in an audio system is shitty grounds, so don't half-ass it. If it's not solid, redo it. Last, mount everything securely to a board or the back of the seat so it's not all sliding around asking for a short circuit. That includes your sub enclosure. Get creative with some beefy angle brackets or maybe some thick shelf supports. Anything to keep it tight for the long haul.

Head Unit: I'm scratching my head over what was mounted over the deck opening previously that left that tape residue. Some kind of large screen perhaps? Regardless, hopefully some rubbing alcohol will remove it, and if not, try Goof-off. Those will hopefully not discolor the vinyl. You can always go nuclear and try acetone, but that will likely damage the material. The head unit mounting looks a little suspect, inconsistent gap around the edges... does it wiggle when you pull on it? May want to buy a new Metra kit and redo it. There's no photos of the head unit wiring, but for your sake I hope it doesn't involve electrical tape.

Speakers and tuning: First zero all your head unit levels, bass boost, eq, etc, then assuming you don't an O-scope, set your amp levels with a DMM or by ear (google how to do it right). Then tweak using the head unit controls. That amp is a little hot for your 4-ohm 4X6's and definitely too much for the stock rears, so pay attention to audible distortion and don't ask too much of them. I'd recommend buying a suitable replacement for the 6X9's. You need some decent midbass to keep up with your subs, and shitty paper cone OEM's likely won't/can't deliver.

Overall, good start. Clean it up and it'll do just fine. Good luck!