There's lots of things to go on. There's his own eyes from watching the pitcher's body language, actual results, how many pitches per AB, starting with strike 1, starting with strike 1 on different pitchers, staying out of patterns, talk to the catcher, talk to the MIF on how much balls are breaking, watching body language of the hitters after striking out or judging on how hard balls are being hit.
Most of the time though when a manager is yelling about balls/strikes it's because he's hearing it from his own guys that the outside/inside corner is huge/tiny and watching the hitters react to each pitch.