After you reach Wutai, and after you find Yuffie and take back your Materia; you can then enter the Wutai Pagoda. The Wutai Pagoda is a Pagoda consisting of Bosses On each level. All of the Bosses are extremely easy. When you battle each boss, you have to only use Yuffie as your only character. The Pagoda shouldn't be that hard. Make sure you equip Yuffie with your best materias.

When it demands it, Make sure you heal. Yuffie should use Cura or Curaga depending on how far along in the game you are. This battle is harder than the first two, he depletes your HP and attacks. Make sure you keep up Attacks and Magic. Cure When Done.

Wutai Pagoda Bosses
Gorki	This guy isn't hard at all. You shouldn't even have to use any Magic Materia when you battle him. Keep up the Physical basic damage attacks, and he shouldn't be a problem. Heal Up when you defeat him.
Shake	Again, not as hard. Keep a Strong barriage of Physical and Strong Magic. Make sure you don't cast any unneccessary magic. Cure after or during this battle.
Chekhov
Staniv	Less hard than Chekhov, this battle shouldn't be hard. Keep Up attacks and Magic. Make sure you Heal when done.
Godo	Yuffie's Father, shouldn't be too hard. Like the other battles, Keep Up Attacks and Magic.