I gotta give props to you “computers” out there that have mastered the art of baserunning. I can’t tell you how many countless innings I’ve run myself out of this year. They’ve changed it so drastically this year. It’s really hard for me to get used to. I’m goin back to station to station.
All you have to do is learn how to run the bases manually using the left stick and the base buttons to advance each runner separately, and don't get greedy/fancy/cheesy to try and bait a throw or you'll get backpicked, and you'll be golden.
Use classic, never ‘advance all’ and soon you’ll be a computer too!