When Dr. Zomboss comes down to throw an ice ball or fire ball, use Freeze Shrooms to freeze him. This gives your various pults a chance to get some damage on Dr. Zomboss himself. Jalapenos will also damage him when he is down to toss a fire or ice ball. The more damage you can do to Dr. Zomboss, the quicker and easier the level ends. Keep at least one Freeze Shroom and one Jalapeno on reserve for whatever he tosses.