Does it matter which blanket I take below and which one above when I cover myself with the two? If I take two blankets together, one is more insulating and the other less insulating, to cover myself, does it matter which one I take below and which one above? Will there be the same amount of heat under the blankets together? 
 A: In a still air environment, the previous answers are correct and sufficient. In an environment with  unheated air moving over you, however, the answer greatly depends on what blankets you have, exactly. Humans lose a lot of body heat to evaporation of sweat, so the amount of air passing across you makes a big difference in how warm you stay. Let's play a game of extremes here and say that your two blankets are:
1. A thin sheet with very little insulating value but low permeability.
2. A fluffy blanket that reflects most of your thermal radiation but is highly permeable.
If you wrap the thin blanket around you first, and the fluffy one second, you will lose a lot of heat to convective currents. The thin blanket will readily conduct heat to the air above it, which is not well trapped by the airy, fluffy blanket above it and can easily carry that heat away.
If you instead wrap the fluffy blanket first with the airtight one around that, you create a pocket of still air around you which is also very insulative. The air around your body stays there, as does a larger portion of the heat you deposit into it.
Note that the same principle applies to the blankets individually; a thin sheet wrapped loosely around you will keep you warmer than the same sheet wrapped tightly, because more of your body heat is stored in the air around you rather than conducted into the sheet then carried away by convection and evaporation.
A: On the long run both scenarios will be equally as comfortable. However, when you initially cover yourself, you would want to cover urself with the thicker blanket first, so that you restrict the movement of air as much as you can, and thus warm up a few seconds faster. This is key because your body will warm up the air directly above your skin and the thick blanket will keep it from escaping much better than a thinner one.
Edit: Thicker does not necessarily mean more insulating, as @annav correctly points out in her answer, so maybe more generally you would want to cover yourself with the more insulating blanket first, for the same reasons as above.
A: The type of blankets is not defined, different can mean many things.
If one makes two classes, more insulating ones and less insulating ones the answer of Photonicboom applies. The more insulating one next to the skin will give a comfort value sooner than the less insulating one because the body will have to heat up a smaller amount of matter (air and blanket) around it. For blankets made of the same material the thicker the better in capturing and heating the air around one fast.
A blanket may be thinner but much more efficient in trapping the heat around the body than another type of blanket ( consider those thermal units for people rescued from ice).
A: Whilst I'm not sure that I disagree with what has already been written, I think  that there is another variable - the temperature of the ground.
I do a lot of cold weather camping, and it doesn't matter how thick your sleeping bag is, if you are not properly insulated from the ground with a thick sleeping mat, you get cold.
Presumably this is because heat conduction becomes very important in such conditions, so I would have the thicker blanket on the bottom. In other words, I would double up the thick blanket and lie on it inside the thinner blanket (if the ground were cold).
Edit: I realise I've possibly misunderstood your question, but perhaps you could clarify what you would be sleeping on.
