The middle heatspreader is kind of a pain to get to without seperating both boards. I just leave the middle on alone. But, yeah, the bottom heatspreader should be removed, and actually replaced. When you replace the thermal pads (on each side of the bottom heatspreader) with epoxy, you actually lose almost 1mm of thickness (yeah, they're that thick). See the image below for more of a pictoral explanation:
It's not hard to do and well worth it IMO. I just had the thermal pad let go on my Quark recently and was floating around in the case.
By the way, you shouldn't need a lot of adhesive. It's supposed to be a very thin layer.