waterproofing over living area

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waterproofing over living area
i have a client who wants a garage with a flat roof which he is basically going to use as a deck.  he wants to use wood decking.  can someone point me in the right direction on how to waterproof this?  i am planning on putting plywood over the framing and place some sort of waterproofing membrane over this, but once the deck screws puncture this, doesn't the membrane lose its purpose?
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what you want to do is create vertical columns stubbing up from the roof (that is waterproof) and then build a wood deck above the roof some distance.
the columns can be flashed properly to prevent moisture from getting through.  also, the deck should be built in such a way as to allow future access to the roof should a leak occur or a new roof be needed.