WELL... big subject this, i really must recommend going thru as many build logs as you can to see how others have done it, if you check out my charade build
HERE you can see the inside of my enclosure and how we secured the baffles/ports, mine is a bandpass, so not necessarily what you'll be doing, but it will give you a fair idea at least...
basically to build a proper wall, your enclosure needs to be coupled with the body extremely well, and all gaps around the box sealed up airtight... whenever somebody asks about walling their car, i usually give them the reply that to properly wall your car, you must be willing to write off the car... now this isn't always the case, if you look at the phoenix gold astra, everything in that car is 100% removable, but as Scott will tell you, it was VERY arduous task building it removable...
in reality, it is almost impossible to wall a car, and not have to drill new holes into the body, you can do it, but at the sacrifice of strength, which IMO, is one of the most important aspecs of a wall...
making a good seal between the enclosure and floor is usually done by building the enclosure on the floor, and screwing/bolting it into the sheet metal, sides of the enclosure are often screwed/bolted into the inside of the C/B-pillars and the roof of the enclosure is usually wedged in position then screwed into place, this can be done via the back doors in a 4 door, or removing the rear side windows in a 2 door
once you have the shell in place it's a case of making it STRONG, which involves adding extra layers of MDF to the insides usually 3-4 layers of 18mm for the shell and back, then the baffle can often be twice that for a big numbers car...
your port arrangement will basically depends on what you want to achieve from the car, if you want loud musical then a bandpass, or central port works well, if you're primarily burping the car, and wanting numbers, then having the port on the drivers side is the way to go... quite often the port on a nubers car will simply be the width of the baffle itself, which is where an 100mm+ baffle really comes in handy...
all in all, a wall is definitely not for the faint hearted, but ALOT of fun to build, and even more fun to enjoy whilst cruising around...