This is usually the way it works in the PC world. I'm going to be doing the same exact upgrade soon. I'll probably put the 2x4GB sticks in 3 & 4, run geekbench, then put them in 1 & 2, and run geekbench again. Then go from there.
I put the the 4GB sticks in slots 3 and 4 and when I booted up the computer the RAM utility popped up and said that for optimal performance I need to put the 4GB sticks in slots 1 and 2 and 1GB sticks in slots 3 and 4. Hope this helps.