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*dies* They're the same. o.O The syllable -fi is pronounced the same as -phy. Either spelling is okay with me, though if I had my way, it would be Manafee, like manatee. ^^ I like manatees.
If they translate the name directly, it will probably be "Manaphy" in English. However, I prefer spelling it "Manafi". I just think it looks better that way.
I would use Manaphy for the sake of spelling. XD Since I would normally pronounce them the same either way, Manaphy just looks more formal (for the lack of a better word O.<). X3