you don't have different sets like hitting and pitching (total control vs. classic for example).
but you do have a few ways to move guys around with the standard configuration. you can use the right analog to point toward the base you want the guy you're controlling to go to.
so say there's a ball in the gap and you're on first, you can push to 9 o'clock on the right analog and you'll go straight to third.
The triggers will also control one player station to station. The shoulder buttons control all players station to station.
And you can use A to switch between runners.
IMO running is pretty well done, especially stealing.