Sub in trunk + wood + air setup... How would I approach this?

NorthStyle

The only bad part about "theoretical" builds is that you don't have any actual parts on hand to measure... which is probably the most important part of an install. A sub + enclosure, and an air setup (depending on what you want will have a 3-5 gal tank + 1 or 2 compressors and all the associated hardware) takes up a lot of space in a car with not much of it.

My air setup fits in the small area behind the seats, at the front of the hatch. But, I only run a 3 gal tank, and a single 480C compressor since the air is limited to the front axle. If you're doing all 4 wheels this tank wouldn't be adequate IMHO. For a sub/enclosure, since you're wanting an upward firing I'd look into the Wicked CAS spare tire boxes. Depending on your model they can fit either a 10 or 13-in sub, so not too far from what you originally wanted. For the wood flooring, I'd do that last once you have everything in place. Use the trunk carpet to make a template with cardboard, cut the wood, test fit for adjustments, cut again if necessary, laminate it, install. Done.... but this is if you wanted most things hidden. If you want everything out in the open then you'd probably want to do the wood earlier in the process.