It depends on what kind of setup you want. I wanted to have an amp rack in the floor of the trunk. But I also wanted to have access to my spare tire. (which I wanted to keep in the car) So I built my deck about 4 inches higher than the original, and hinged it right in front of the speaker box. Now all I have to do is pull up and it opens so I can grab my spare.
But if you just wanna mount your speakers in the floor of the trunk then it's easier to just relocate the tire underneath...