Some people put fat side up because they say the melting fat bastes the meat. The extreme version of this is "barding," where you wrap the meat in fat.
I've never seen any tests that prove or disprove this, but my own experience seems to support the notion that the self-basting effect is minimal, if it exists at all.
So, I always cook, whether in the smoker or in an oven, with the fat side down, but I do it for one more reason: I like to spray the meat with sugary liquid during the smoke, both to increase the smoke adhesion, but also to help build up bark. This spraying would be wasted if the fat side is up, since I discard the fat at the end of the process.