I guess it might make a difference from one manufacturer to another, but on Bridgestone tires the red mark goes next to the low point indicator (some are dimples, some are little weld beads like this thread has). If the tire only has a yellow dot, then that one goes next to the valve stem hole.
Heres a link that explains the dots and what they mean.
http://www.bridgestonetrucktires.com...0ask%20doc.pdf