The reason the pick-and-roll is working with Chandler and not Amare is very simple. Spacing. Defenses still have to respect Amare's outside shot. When he is at the top of the key, he draws a defender, allowing Chandler the space to roll to the basket and Lin the space to pass it to him. Chandler's outside shot is not a concern for defenses. His defender will always be in the low block creating too much clutter for Amare to roll and Lin to find the space to pass it to him.
With that said, Amare doesn't need to come off the bench. When he and Chandler are on the floor together, or Chandler and Jeffries, run the pick-and-roll through Chandler. With the option of kicking out to either Amare or Melo. When Chandler goes to the bench, move Amare to Center, with either Melo or Harrelson at PF, and run the pick-and-roll through Amare.
Very simple. With this approach, and better outside shooting from SG, we will see much greater production out of Amare, and everybody else, in my opinion.