I can't claim to have done extensive "both ways" testing, but my feeling too is that the pad on top is warmer, for just the reasons previously cited.
I used a setup similar to Ryan's on the AT early this year, when temps got down at least some days into the teens. I had the (size regular) neo-sandwhich, for me a 1/8" thinlight below and a 1/4" thinlight above, and from *brief* testing I felt warmer with the thicker ccf pad above (even though it is arguably more comfortable with the neo on top). I was prepared to stack both pads on top if it ever got cold enough to warrant that, but I don't think there was a night when I actually did so.
Clothing, bag etc: 20F WM bag, Montbell alpinelight parka, feathered friends down booties, cap 1 longjohns.