By default, the lead runner (runner at second) will be selected. For me I'd just pull the left trigger once which will change the runner's icon to 'H' and he's heading home. If by chance, you wanted to send him home and also send the batter to second, you could just click the left bumper once and ALL runner would advance an extra base. The key for me and my baserunning is remembering that the lead runner is selected by default and I just use the left trigger to advance one and right to retreat one.