as far as i know it will only run dual mode if its in 1/3 or 2/4. Bios should tell you on the diagnostics screen at boot-up if its running single or dual.
If the computer is telling you that it runs in dual channel when it's in slots 1 & 2, then run it that way. My motherboard runs in dual channel when you use slots 1 & 2 or 3 & 4 together.