I'm with Coachric in that a lot of this should be taken care of during practice but sometimes things pop up that need to be addressed.
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1. Stealing signs - when you notice a team working hard to pick up your signs (and, for example, pitching out on just the exact pitches you're stealing) do you prefer to change signs between innings, change indicators, add/change a wipe off sign, or what? What's your preferred method?
On this we usually wait until the inning is over to change the indicator. I really don't give that many signs to begin with so it's hard to pick ours. What cracks me up is the 3rd base coach who gives dummy / false signs to the leadoff batter before the first pitch. Teach him what to look for in practice so he knows to do it without a sign.
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2. Multiple runners - if you have runners at 1st and 2nd and a ball is hit to the outfield, how do you handle giving signs to both runners? Say you want to send R2 home and hold R1 at 2nd base?....do you use right arm/left arm or verbal for one and sign for the other?
Always go with the philosophy "you are scoring until a coach stops you". Now you take one decision out of the equation. I turn my guys loose on the bases and they only pick me up when they can't see the ball.
Trail runners are completely on their own until the lead runner passes me. Then I am only going to stop them or tell them how to come into the base.
I got four signs when they approach the third base bag
1. Windmill - they are scoring / advancing
2. Two arms up - stop at third but round it and find the ball
3. One arm up and other arm point at the base - stop on the bag because a throw is coming but it's not a bang bang play that needs a slide
4. I crouch and point at a corner - throw is coming and they have to hurry to the bag and slide. In certain situations I will even have them slide to the side the ball is coming if I feel it will cause the fielder to have a problem catching it (usually this is on direct throws from the OF where the steam has left the ball - if it's a good strong throw with some steam I'm not going to put my guys in the way of that).
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3. Sending/holding runners - do you have a general rule of thumb on sending R2 home on a single (obviously weighing the arms of the outfielders and situation in the game)? For example, do you use the timing of the fielder getting the ball and R2 touching third base as a general guide?
This one is harder to answer because there are so many factors - runner's speed, arm strength, how hard hit, direction hit, field conditions etc... - I guess I look at runner speed and arm strength the most but I'm aware of the other factors too. I guess what I am saying is you will learn this from experience of getting guys thrown out.
There are two kinds of third base coaches - those who got guys thrown out and those who are going to do it shortly. It happens but don't let it get you away from your philosophy.