Do this for about three minutes, then collect the balls and work on 5-3, 6-4, and 4-6 plays for another three minutes. This is followed by hitting balls to the 5-6 hole. If the third baseman doesn’t get it, he retreats back to third, and the shortstop flips to third for a force-out, rather than throwing across or turn a long double play. The other fungo batter hits balls to the second baseman, who works on throwing to first.
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Next, third base fungo hits to left, who throw to second, SS cuts (make a few of these the "cut off a double on a ball hit into the corner" variety - timing becomes important here, as the other fungo needs to hit many fewer balls than the fungo hitting to left). First base fungo hits to right, who come home, first baseman is cutoff, 60' from home (about pitchers mound - this postitioning puts him out of harms way should the SS overthrow second). On the throws home from right, make sure that they are the "normal" kind - hit the cutoff man, and don't hit too many. The right fielders will get to go again, as they're last throws will be the "do-or die" variety.
Break your team up into 2 or 3 teams. If you do 2 teams you’ll need 8 or 9 on a team with a player for each defensive position. If you only have 8 on a team you can eliminate either the pitcher, catcher, or one outfielder based on what is a priority for your team that day.  If  you only have 12-15 players on your team break it up into 3 teams of 4-5. Then place two of the teams on defense and one team hitting fungoes. No matter what, have the teams and batting orders pre-made before practice. This will eliminate unnecessary downtime during practice.
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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.”
If your high school or travel team has at least two coaches, you can use what Bates calls a two-fungo drill. One coach can hit to third and second, while the other hits to short and first. If catchers are finished working with the pitchers, they can feed balls to the fungo hitters. The idea is for the third baseman to practice turning a 5-4-3, with the first baseman moving up toward second base about 60 feet instead of 90, with a net behind him to catch overthrows. The shortstop works on throwing across on 6-3s.

For starters, we should clarify just what we’re talking about when we say fungo bat. Longer, lighter and thinner than a regulation bat (but a larger barrel), a fungo bat is typically 35 to 37 inches long, and weighs between 17 and 22 ounces. As David Allison wrote in the June 1978 edition of Country Journal, “A fungo bat looks to be a cross between a baseball bat and a broomstick.”