As I'm thinking, you may also be wondering what to do with your stock battery cables, the positive and the negative. So, just in case you are, here's what I did, and a couple ideas on what you can do.
What a lot of people seemed to do when I was doing research was to leave the stock cables in place, and just connect up the new cables to these cables. In other words, the new battery cable from the battery in the trunk runs all the way up to where the stock positive cable is, the two get connected together somehow. This will work if you decide to do this, just make sure that no wire/terminal from the connection is exposed (obviously). For the stock ground, just find a way to bolt it to the car frame/body. Don't leave it hanging, you should ground it.
Another thing you can do is remove the cable altogether. The stock battery cable goes to 3 places. Here's a quick pic of the stock cable (it's the red one cut in half, the battery connector part is on the left side, starter post connector on the right side):
You have the battery terminal connector (the red boot on the left side of the red wire in the above pic). From there, there are 2 cables: 1 goes to the fuse box (the short red cable on the left side), and the other goes to the starter (the long red cable, which is cut).
You can remove the stock positive cable,
as long as the new battery cable from the trunk goes to the fuse box and starter. In my case, I used a power distribution block (as seen in my previous post) to split the battery off to the starter. I then used the jumper stud to connect the battery to the fuse box. You can see this in the diagram I put in that previous post.
The alternator cable, which I'll show in a second, goes from the alternator to the fuse box. So you could technically leave this cable in if you don't want to replace it. Just make sure, if you do alter the stock positive cable, that you reconnect the alternator cable to the fuse box. Here's the stock alternator cable:
And the replacement alternator cable:
The left side connects to the alternator, and the right side has two fusible links that connect to the fuse box. In my case, I opted to replace the alternator cable with a larger gauge one (because of the small battery). So I used 1 size larger AWG cable, and 1 size larger fusible links (orange is new cable, other is stock):
And then just used a boot on the alternator side:
So, in summary, you can quite easily remove the stock positive cable, as long as you ensure that the battery goes to the fuse box and starter.
For the negative wires, I opted to leave the stock one in place. It goes a couple different places and it never hurts to have extra grounds, so I just left it. I cut the battery terminal off of it, put a ring terminal on it, and attached it to the negative jumper stud. I also ran an additional ground from negative jumper stud over to the driver side shock tower. It's a little hard to see in this pic, but the negative jumper is the one closest to the front of the car (with the black boot) - you can see the stock negative cable coming out of the jumper - it's the dark black one that doesn't have split loom on it. And the other one without split loom, that looks like a smoke clear jacket with wire is the additional ground I added from the jumper to the shock tower:
In this pic, you can see the additional ground I added better (no split loom, looks like it's not factory cable), and if you look at the shock tower right above the fuse box lid, you can see where I removed the paint and attached the cable via bolt (make sure you spray clear coat on it afterwards to keep the bare metal from rusting):
