Sorry, no absolute clear cut answer. Reasoning is given below if you really want to know.
Its Thermodynamics %'s. Whichever orientation gives the 2nd pad closest to the ground the smallest Temperature gradient. From one side being the "Hot" side to the other being the "cold" side. Of course this is too simplistic really.
Air mattresses without down in them create air currents transporting heat(convection). So, is said R-value of said air mattress given with said convection tabulated or did they "calculate" said R-value with conduction only?
Its calculated with conduction only and NOT Convection. This is a base Lie. It depends on temperature to determine how bad of a lie it is. Why most air mattresses come with foam inside.
Why? Convection depends entirely on HOW large the temperature differential is and therefore cannot be stated accurately for the common Jack/Jill to understand. The convection actually transports MORE heat than conduction. Therefore said air mattress R-rating are base lies. I used to carry one, I can vouch for that much! I now carry foam. Foam doesn't leak either!
So, back to initial statement. It comes down to %%%. If your air mattress transports more heat than your closed cell foam pad then it goes on the bottom and the foam pad on top. Therefore there is a SMALLER temperature gradient delta in said air mattress to create said convection air currents inside the air mattress. Of course this depends on how THICK your foam pad is. If it is very thin then placing said air mattress under you first would be preferable with the foam pad on the bottom.
If on the other hand you have a super thin down filled or equivalent air mattress and also a foam pad then it gets quite a bit more complex.
Sorry would really have to know EXACT setup and actual test environment. Consistent ground air temperatures in other words.
MOST people I know if they bring an air mattress, usually bring only a "half" air mattress and put it on top of their closed cell full length pad. Of course some cheat and use rope/slings etc at foot pad and don't bring full length pad at all, but rather bring half length closed cell foam pads. Besides half length closed cell foam pads are great for sitting on during a rest break. You wouldn't dare do so on an air mattress as you would quickly have a hole in said mattress.
Sorry, no absolute clear cut answer.