I've done both, amp on top and on bottom. (Same applies to my Receivers). Always try to put them in a spot where I can leave them by themselves, or put them on top of other components so they have room to disipate the heat. I would like the amp to be on top, so you can see the meters, but currently with my setup, even though it is on the bottom, they are still viewable without too much effort. I the try and put the components I use the most towards the top, i.e. preamp, tuner. Turntable, obviously is on the very top of the rack so I can raise dust cover and deal with the albums easily. Also, I try and go/look for a "flow" to the components in the rack. Again, as you said, it is mostly preference. (Also, try and separate the amp from the preamp, the tuner from the CDP, just to help eliminate any noise pickup from either component.)