I agree that the stain probably originated from the trunk and not the spare tire well, because the fluids would have dripped down. The stain on the carpet would have had to have been the result of the fluids seeping up all the way through the pressed board cover in order to get the carpet stained, from the underside up. Unless (and this is hard to type) the bag had ripped on the top, and the body was stuffed so hard into that little space with a great deal of weight placed on top of the carpet and board that the fluids would have to have literally gushed out in order to saturate the board enough to get onto the carpet above it. But the board didn't seem to be saturated all the way through to me. Plus, those types of boards tend to have some sort of coating on them that kind of waterproof them, so it would have had to have been placed in there upside down in order for the top to have fluid on it.
Now there is a possibility that Caylee had been in both places, I try to imagine the stress Casey was under knowing there was a body in the trunk ( I know how stressed *I* get when I've accidentally forgotten my wallet and I'm driving around without my license, I just KNOW that I'm going to get stopped!) It is possible that she tried to stuff Caylee in that space at one point or another, but it seems that the by the time the decomp started seeping out Caylee was in the trunk and not the well.