When facing Bowser (both the first and second times), make sure you have Bombettie in your party. Also have a Plus Power and a Plus Defense badge. When you enter the battle, use Bombettie's Bomb (it is only 3 FP and it does good damage). You should do 6 damage in the first battle and 5 during the second. Have Mario heal himself and use moves that do not use FP. In the second battle, the Stars help you at the start. When you enter, make sure you have around 40 HP. Your FP can be down -- do not use any items to heal your FP. Make sure you save Star Power, use the Elder Power when Bowser uses his claw attack (it will poison you), and keep your health up. Bowser's health during the first battle is only 50, and is 99 during the second.