First base fungo hits fly balls to center field (helps here if both fungo hitters move up and apart, hitting from about the front of the mound extended towards the bases). Center throws to second, second baseman is cutoff (for us it was, anyways - change to suit your style). Third base fungo hits balls to left field, who throw to third, with a second shortstop as cutoff (but you really don't need one, if you're shorthanded).
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Even in those formative years, authorities on the game warned the practice of hitting fungoes should be limited to coaches. Henry Chadwick, one of baseball’s earliest proponents, claimed “The weakest batting is shown when the batsmen indulges in fungo hitting,” according to the Art of Batting. Others agreed that the practice was bad for training a batter’s reflexes: “While watching some of our freshmen practicing ‘fungo’ batting the other afternoon it occurred to me that it was about the worst kind of practice a batsman could imagine in training his eye in batting,” a writer claimed in the March 3, 1886 edition of The Sporting Life. “It trains the eye to meet the ball in batting it in a manner which never occurs in actual play. It ought to be prohibited on every well regulated ball field.”