That's what I want to do only using CPU fans, but I don't want them
protruding from the bottom. That's why I thought about insetting then into
the heatsink. I think I may be able to mount them with the CPU heatsink
directly to the pills, but I would need to do some measuring to make sure I
can mount them without shorting anything out.

There is a much better heat transfer from the metal base then
blowing air over the white cap. Just blow air INTO the fins.

Do you feel cooler sitting in front of a fan or behind it?