Push the left analog stick toward the runner you want to control. In this case, left. The icon representing your runner on third will start to blink in the baserunning window indicating he is the one you will be issuing a base running command to...
Now hit the base you want him to advance to... In this case, X.
O = 1rst
A = 2nd
[] = 3rd
X = Home
You can use this scheme while runners are on base or moving on the base line (just make sure the icon is blinking in the base window first) to advance or return to a base or multiple bases. For example, if you thought the fly ball was going to get passed the outfielder and rattle up againt the wall, you could hit left to select the runner on 3rd and hit X to send him home, and then push right to select the runner on first and hit X to send him home. Now you can sit back and watch. But as the runner from 1rst is rounding 2nd, you see that the outfielder got to the ball faster than you expected, and you realize your runner will be thrown out at 3rd. Now you push up (i.e. toward that runners icon in the base running window), and when his icon starts blinking, press A to send him back to 2nd.