Remember, those are overall sizes. The actual top and back were cut from a 48" piece of material, and after adding the end caps, which are made out of the same 1/2" MDF, the overall dimension is 49".
To install the box into the car, you'll need to position it to where the front of the box is pointing downward, then maneuver the box into place and turn it back to right-side-up. The 4"x6" size cradles perfectly behind the wheel well.
Next, you're going to build the side speaker boxes. These serve as more than just to house the speaker. They will also keep the big box in place by wedging it between the wheel wells and the back of the car. It's much easier to build these pieces out of 1/4" MDF as then it is not as important to cut the edges at saw-cut angles. However, the back of these boxes needs to be 1/2" material because they are what will be bolting the box into place.
These side speaker box enclusures only have 3 sides - a top, front and back. Creating the top piece is the tricky part. The front dimensions are 8" wide by 7-1/4" high. Cut that piece out first. Place the subwoofer speaker box in the car, making sure to position it exactly how you want it to sit in the car - all the way back, with the top just below the sliding shade. It should naturally sit like this if you built it to the dimensions I listed. Then, hold the 8x7-1/4 front piece in place, against the speaker box and against the wheel well. While holding it here, trace a template of what the top will be shaped like. I used 1/8" depron foam to build my template. This part is slightly difficult, but the good news is you can just mirror image your template and build the other side.
Once you cut out the top piece from the template you drew, you need to attach it to the front piece. To do this, you'll need to use some kind of CA (SuperGlue) and kicker (a spray that makes CA dry instantly). Holding the 2 pieces exactly how they need to be, use a liberal amount of CA and kick it to make it instantly set. Then, take a pencil and from the underside of the small box, trace along the top piece and front piece onto the subwoofer box. So now you'll have a pencil outline of exactly where the side box needs to sit. Using this tracing, build the back of this side box out of 1/2" MDF.
Now assemble the side boxes. The top and side are already secured with the CA. Use wood glue and finish nails to secure the back to the top and side. Let this fully dry. You might want to install a gusset to the top/front joint to make it stronger.
Now, trace the speaker cut-outs and cut out the holes for the speakers. You will use the speaker hole in the side boxes to run a couple screws through the back of the boxes into the subwoofer box.
The next step is to cover the box, before you bolt the side box pieces to the subwoofer box. I covered mine using black automotive carpet. Once the boxes are carpeted, install the subwoofer into the box, then install the box into the car. Then, hold the side boxes tightly in place and drive a couple self-tapping screws threw them and into the subwoofer box. Be sure to position them tightly against the fender wells, as this wedge is what holds everything tightly in place.
Now just bolt in the side speakers and wire it all up. If you ever need to remove the box, you just have to remove the side speakers, then unbolt the side speaker boxes from the subwoofer box. Then you can remove the big box.
