sub, 2002 jetta

Okay I bought a new car yesterday and I was looking to hook up the subwoofer system I just bought for my old car into it. The only problem is the trunk area. The floor in the trunk is covered totally by a soft mat that needs to be removed to access the spare tire, also the floor around the tire is not that large.  I want to retain access to by spare tire, because being stranded in the middle of nowhere is not an experience I really want to have. My main question is whether or not I need to worry about the fact that some of my box will hang over the dead space above the spare tire and not be on solid floor? I was thinking about making a removable subfloor out of mdf to mount the box and amp rack on, but I wanted to know if this would be necessary before I went through all the trouble.

Haha, I have AAA myself, and incedentally just had to use it last Sunday because I hydroplaned into a curb and flattened my tire (on my old car). The fact that I made my first sub box so that I could access the spare tire saved me a lot of headache, however. Free towing or otherwise, I had already driven a half hour to do some things for my mom, and I would have been mad if I had wasted my time and had to spend the day trying to find a shop open on Sundays to fix my tire.