The amp will generate a lot more heat than the CD player, and as warm air rises, it would make sense to put the amp on top of the CD player. Moreover, the ventilation holes in the amp case's top won't be obstructed.
As an alternative, you could try doing what I did for my grandfather a few months back. His TV sits on top of a kind of drinks cabinet piece of furniture. I went to B&Q and bought a piece of melamine board, precut and finished on all edges (they call them shelves) and four RIGID door stops. I screwed the rigid door stops to the corners of the shelf piece and made a little table with about 2 1/2 to 3 inches underneath it. His DVD player sits underneath and his new 42-inch LCD TV sits on top the shelf. I'm going to do the same tomorrow for my bedroom TV and DVD and I'll post a picture if I can figure out how.