Most importantly, leave adequate room for excursion of the woofer, so that you are NEVER having to worry about the surround coming in contact with the floor. If the sub that you are using has a peak to peak excursion of 1.5", allow for the height of the surround (above the mounting surface), and then add .75" for movement. I would do extra to be on the safe side.
Secondly, how much room "can" you allow? I ran down-firing 12s in my Sierra in a prefab box, and there was an opening in the front and on the sides. This was only about an inch off the carpet. This was with an internal mounting depth maximum of about 6", if I'm not mistaken. I found that I got significantly more volume and "effect" from the base, by propping the box up slightly. I got a couple of round plugs from Lowes, which were about an inch tall, put one under each corner, to hold the box up. This worked nicely until I pulled it and gave up on the whole under seat box idea.
With all of that said, I would leave as much open room as possible, without killing all of your mounting depth. If you move the bottom board up, creating more room, your mounting depth will be reduced by the same amount. Know the subs you are going to use first, then build the box for the subs.
Hope this helps.