WITH A RUNNER ON SECOND
With a runner on second base you have to be extremely careful and disguise your signals so the runner cannot relay the pitch and/or location to the hitter. The most basic way is to put down a series of numbers. Only the pitcher and catcher know what the "key" is to figuring out the meaning of the signs. The easiest way to explain this is to provide an example.
We will use the same signals from Common Pitch Signs and Type and Location sections. The catcher will put down a series of signs (4). Using his fingers he puts down (2,1,3,1). In our example, only the first two signs will mean anything to the pitcher. The first sign is the pitch and the second sign is the location. Seeing the signs (2,1,3,1), the pitcher should know to throw a curve ball (2) and outside (1). The (3) and second (1) mean absolutely nothing. Now try and figure out this sign combination: (1,1,4,2). The answer is a fastball outside. Again, this is just a basic example. Sometimes the keys can be quite complicated. This is especially true at the college and professional level.
The key is the keep the signals easy to understand for both the pitcher and catcher, but difficult enough that a runner on second will not be able to steal your signs. If you do catch a runner stealing signs, call time out, talk to your pitcher and change the signs.
http://www.baseball-catcher.com/guide/signals.htm
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SIGNALING PLAYS
The catcher is responsible in most cases for calling plays in bunt situations as well as first and third situations. Before the pitcher steps on the rubber, get the play from your coach. Step out in front of home plate so your teammates can see and give the correct signals. The signals can be verbal, a series of signs (hand or body), or both. The purpose is to disguise the defensive play and put pressure on the offense to execute.
PICKOFFS
Pickoff plays vary from team to team and coach to coach. Some plays involve only the fielders and pitcher. Other plays depend on the catcher for the attempt to be successful. The most common pickoff plays are to second base. One of the more popular plays is the blind pickoff. This pickoff gets it's name from the fact that the pitcher is not watching the play and relies on the catcher to signal when to turn and throw.
On the blind pickoff play, the fielder (usually the shortstop) will signal the play to the catcher. Maybe they notice the runner is not paying attention or is getting too big a lead. The catcher must then notify the fielder or confirm the play using a subtle signal. Now, signal the pitcher that the play is on. The pitcher must go through his usual routine so the play is not tipped off to the other team. The pitcher should then be looking at the plate and not paying any attention to the runner. This is a timing play and the catcher must read the middle infielder breaking for second. At the correct moment, signal the pitcher to turn and fire to second. The signal can be anything you want. We usually use a glove signal (dropping from the receiving position). The blind pickoff relies on the catcher's timing of the fielder reaching second base for a successful attempt.
http://www.baseball-catcher.com/guide/misc.htm