I never heard of the books until a month or two ago. But during the pilot, I paused it every 5 minutes to wiki the new characters. Now I have a pretty good grasp of the universe so far. Didn't need to do that in the second episode.
As far as who to root for, I'm guessing the Stark family, Daenerys, Jon Snow (the bastard), and Tyrion Lannister (the dwarf).
Viserys Targaryen (Daenerys' brother) and the Lannisters (incest twins) are looking to be the baddies.