best place for a 12" in a stack wagon cargo area, IMO would be in the storage cubby on the drivers side, or underneath the fold up cover for the third row, but you would have to do some work to make it look right and not rattle all to hell. If you do it in the foot well of the third row you can either put some venting in the cover, or you can make a box that sits below the support rails for the cover, and just leave the lid up when you want subbass.
I kind of did that last part, but a little more extreme, I put an 18" sub in that spot, but the back of my wagon whas been seriously hacked apart and modified throughout the years.
I had to raise the floor about 5" to do it like this, but it works
its almost finished, and it just needs carpet, the amps and the subs are completely covered by a false floor now, with a grill over the subwoofer
but for a single 12" you should be able to make it fit underneath the cover pretty easily