EPDM

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Putting a deck on a flat roof is tricky business. You want to be sure that the roof doesn't leak (would hate to tear up the deck...), the roof can support the deck, and the deck is attached securely without defeating the waterproofing.

EPDM is a great long lasting rubber membrane that is good for this application. Search for EPDM on the web and check out this website. The deck joists can rest on special EPDM or neoprene pads.
http://www.conservationtechnology.com/

Then you must call the EPDM suppliers and roofers to get ideas from them about how to approach your problem.

Bur first -- you need to make sure there is no structural damage or rot from your existing leaks.

Good luck!

Billy