That's one thing about Gigabyte motherboards: for dual channel to work, you have to place them side by side which gives very, very little clearance between the two RAM modules. I have the same setup too, but I guess heat is not much of an issue because my PC is still ticking after 3 years.
.
um no? For the Gigabyte P35-DS3R mobo, the dual channel slots are 1 and 3, and 2 and 4 which means they aren't side by side.