IMO the key to stopping the running game at 2B is to cotrol the runner's momentum.Very few base stealers can steal 3B from a stationary lead.(Yes a ++ runner with a long lead can steal 3B)
Keeping the process simple is imperative so that the pitcher can efficiently execute his pitch which is the key element in the equation.Expediting the process,as bsballfan intimated, is important. The longer it takes, the greater chance the runner at second will have momentum & the chance of of your pitcher being focused on executing his pitch will lessen.
First,have the pitcher look to 2B with 90 degree head turn instead of a 180 degree head turn(may have to add a few degrees if the second baseman is responsibility for holding the runner[RHP*). This allows him to get back to his target faster. If he is a look to second throw to home guy that is not necessary.This shorter head turn gets him back to his target sooner & cuts down the time that the runner at 2B has to extend his lead.
Finally, the most important piece of the puzzle. The SS or 2B is responsible for triggering the pick or pitch.If the SS is responsible for holding the runner( i.e.LH pull hitter )he would start on the runner's right shoulder. The second baseman would start close to 2B ( How close would be determined by the situation).If the SS backs straight back or steps toward the 6 hole the pitcher pitches(He could also incorporate a little backhand wave as well),if the SS backs up toward 2B or steps to 2B ( Could open his glove as well) , the pitcher turns his head home & picks. The second baseman steps toward 2B(can flash open hand), the pitcher picks. If he steps straight back(backhand wave?) or steps to the 4 hole, the pitcher pitches. If the pitcher does not like what he sees, he is not obligated to pitch. He can hold the ball or inside move. This is very simple & clear cut.
You want to add predetermined picks to this( i.e. 1 look,2 looks,no look,inside move) that's fine. Mix in no look pitches,slide steps, & catcher picks into the mix & you will & further control the runner at 2B.Whatever your package contains, do it well.Do not complicate the process so much that you have to spend an inordinate amout of time in practice to perfect it
JW