Well to avoid his attacks use, Mario, and flip to 3-D.
And to attack use Bowser/Thudley and Ground Pound him!
Also if you have a Item that doubles your attack use it!
But here's a hint that goes with all RPGs:
Don't Forget! When in trouble Level Up!
Actually using Bowser + Carrie is much better. Bowser does double more damage than the rest of the party, and with Carrie's help, he is the about the same fast as the others and he can breathe fire in mid air, and it is also easy to jump on his head. The only drawback is that he is bigger and therefore more vulnerable to attacks. Also, buy a Block Block from the Flopside food shop. This makes you invincible for a while, so be sure to get one.