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I wouldn't recommend [prayer] since it costs too much to use… In fact, I don't recall ever having two ATB bars to use, unless the enemy was already staggered and my active character (either Cloud or Tifa most of the times) was beating him senseless. So, a non-active character with two full ATB bars is something I can only dream of (perhaps with the right combinations of Complete materia)!
Cloud and Tifa should do Chakra and Aerith should have Healing+Magnify. Her Soul Drain restores MP, so she should be good to heal throughout the battle. Never cast with the character you're controlling. Switch and pop Sephi, then hit the menu with another character's healing or ability if you're good on health. It took me fifteen minutes to get all three characters to a good health place to go full-throttle (and also Summon Bahamut).