Restore with no All attached to it for starters. Don't unnecessarily waste materia slots, and seeing as Yuffie is alone, no All's are needed. Make sure Restore is at least Level 3, so you have Regen. Make sure she also has Time (level doesn't matter). If you cast Regen while Haste is in effect, the healing process moves faster. Only downfall is it doesn't last as long either, so you'll need to keep putting it back on.
HP Plus' are good, if you have room to spare.
Other than that, just load up the best materia you have onto her. There is no real trick to it, to be honest with you. Level and AP grind beforehand so she is at least... level 25 to 30 I think. Been a while since I did it so I'm not 100% on the appropriate level you should be at that stage.
EDIT: Oh, almost forgot... equip Poison and use it on Godo. Bio 2 at the least. It works on him, and massively helpful. Plus, there's a glitch somewhere that MAY cause it to hit two or three times per turn, doing about 350 / 400 damage each time it hits (totalling to about 800 or 1200 if the glitch takes effect).
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