When I'm multitabling, I try to get one of the "corner" seats -- so that on the table in the top right of my screen, I'm always sitting in the top right corner of the table, etc.
PokerStars sticks you in a random seat each time. But when I play PokerRoom SNG's (which is rare lately) I would always pick the "red dress" lady's seat in the lower left, I just always seemed to have good luck there.