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).
To practice throwing around the infield, Bates recommends several drills you can use. The first involves placing four fielders in a square, about 15 feet apart. The players flip the ball underhanded to each other, like in a double play. Keep their arms straight, using a stiff wrist, with gloves on their hips once the ball is out. Every fielder follows their flip, glove side first, rotating around the square. The idea is to have a sequence of catch, flip and follow. The ball should be caught with two hands, palms open. After about two minutes, repeat the process rotating the other way for another two minutes.