Send more details we may be able to help more. It had been leaking into the apartment below us. Make sure you can lift deck sections so you can clean underneath. Put soft pads between the deck and the roof membrane. If it is modified bitumen we have had excellent results with a quality outdoor carpet instead of building a wood deck that will warp and rot eventually.
Carpet is inexpensive, fast, and easy to keep clean.
Many times looks better than a wood deck. If the corners blow up then use carpet tape that is compatible with the roof membrane, most are compatible.