The final preview item is the gap between the box and the passenger compartment. You'll often be able to see down from the top or up from the bottom. Both the box metal and passenger compartment back wall will be corrugated metal, but otherwise should be totally free of obstructions. Check all the areas thoroughly, since you might be surprised to find areas that are actually made of double metal, sandwiched together and spot-welded. This is an area that adds structural integrity to the vehicle; so don't cut through it without the aid of an engineer who can show you how to alter the site to redirect the forces. This usually means welding additional reinforcing metal to add strength. As a common practice, I'll often weld in a bit of extra 1/8-inch metal just to improve the structure.
Next comes the initial incision. You'll need to map out your cut and drill a pilot hole for your cutting tool. The most often used tools are the metal nibbler, pneumatic metal shears, or with today's thin metal you can even get away with aviation shears if you have the right touch. (This means practice on scrap metal to get the feel of making cuts that are not full of jagged edges). Map out a clean line and drill the pilot hole inside the line. Then insert the head of the nibbler or the jaw of the shear and carefully begin the irreversible process.
A note about the size of the hole: You don't need to cut out a 24x36-inch opening in the panel for anything under six 15-inch subs. A pair of 12-inch subs will do fine with an opening of about 36 square inches (6x6-inch opening). If you don't believe me, feel free to cut the smaller hole and pretest the system by placing your already constructed cabinets against the opening and run it off your system.
You want to prepare the "tunnel" between the box and the passenger compartment. This means filing the sharp edges off of the cut areas and then painting them with a rustproofing material. Unless you live in the dry South, this is essential because water will collect in these areas and cause corrosion over time. Once the rust-roofing material has dried, you'll install some form of tunneling material. This is similar to the material that's used to connect the sleeper cabin to a semi tractor. It looks like two pinch moldings (like on the opening of a trunk) with a rubber section between them.
I've always preferred this material since it has the give necessary to handle flexing between the truck's frame, box, and cab. There are other ways, but this is the simplest, and the most accepted material for automotive use. Press the pinch molding into the opening from the bottom first, making sure it grips securely to both walls. It's meant to grip the metal, which is fine for a flat cut, but with the corrugations in the metal, it'll need to be bent to form with the shape of the surface.
The reason we start at the bottom is so that the seam is at the bottom when you finish. Any falling water will not be able to leak in through the seam. But let's go a step further. The seam should be glued together using an adhesive similar to the glue found in bicycle tire repair kits. This will produce the best watertight seal.
Once you've the tunnel gasket fully in place, check out your work. I generally find that there are a few tiny gaps near the corrugations that I can find with a bright light. For that reason, I'll always use a full bead of silicone sealant over the edge before I install the tunnel gasket for the final time.