The Chargers did not give him much room. I think in order for Denver to be more successful running they have to start out passing the ball.
Thqt is what Elway did in 1997 and 1998. Start out passing the ball get up 7-0 or 10-0 and then start running the ball. The defense will be on their heals. You noticed late in the game after Manning had torched SD McGahee started getting better lanes to run in.
Manning needs to start out the games in a hurry-up offense and DO NOT RUN THE BALL. Pass every freaking time until you get the TD. That alone will open up the running game the next series.