Handling the Pitcher

[Cubbies87]

I had this come up on me in a game, and I didn't really know the correct way to handle it.

I'm umping a 13/14 local game alone. Play under FED rules.

Lefty pitcher, with R1. Batter has one foot in box, taking signs from the third base coach. I have my right hand out, making the "stop" sign so the pitcher does not pitch without the batter in the box (is that the correct thing to do?).

The pitcher is set, and is staring directly at first, ignoring home. He starts his motion, swiveling his head towards home after he starts his motion. R1 takes off to steal second. I still have my hand up because the batter is not in the box. F1 stops his motion, turns and throws to F6 in order to get R1 going to 2nd.

I call time. Place R1 back to first (he would have been out at 2nd), tell the pitcher to make sure the batter is set next time.

I didn't feel the pitcher was trying to quick pitch the batter, and I felt he stopped his motion because he saw me with my hand out. After he stopped, he then realized R1 left, so tried to get a moving runner out.

First of all, what is the correct mechanic for letting the pitcher know when he can pitch if the ball was never dead? Also, if the pitcher starts to pitch at a time when he cannot do so, what is the correct mechanic to stop him?