We spent considerable time designing and detailing these recessed decks to avoid potential issues with water leaking into the structures. To extend the life of the waterproof membrane, we have detailed a system where foot traffic is not directly affecting the membrane surface in an attempt to extend the life and continuity of the membrane.
Our structure in these situation, is a plywood deck that is not flat, but in fact sloped slightly to roof drains. The torch applied roofing membrane is attached to this and extended up the sidewalls up to the finished floor level of the adjacent rooms. This membrane is approx 6" lower than the floor level. We then have a removable wood deck in 4'x4' sections sitting on this membrane. Care must be taken to ensure that the membrane is not being affected by a sharp corner or point load. These wood deck sections are sloped on the bottom of the joists to suit the slope of the membrane, and the top surface is flat. This surface will be approximately the same elevation as the adjacent living area.
In the event that the membrane needs repair or replacement, the wood deck sections are lifted out to access the area. A maintenance free decking like Trex could also be used instead of wood decking.
As an added precaution, it is good to make sure than in areas subject to moderate snowfall, the deck be kept as clear of snow as possible when spring thaw occurs. A frozen drain will be a problem if you get a quick thaw. It is also good if possible to add a scupper in the side wall of the deck connected to a downspout to keep the area dry if a drain is frozen.
I hope this helps. You can also follow the link below on the Fine Home Building wetsite which explains a similar detail.