I'm sure there are many ways to do this, here is what I do:
I always build the deck in floating sections that are small enough so that two men can lift one up and out to effect roof repair. It is generally a good idea to make the deck so that you can remove it and it is NOT ATTACHED to the rubber roof in any way. THis would only create leaks.
I ALWAYS run the joists from the house toward the roof edge so the rain won't be impeded. I figure out how much the roof drops and rip a slight taper in the joists (pressure treated) so that the deck ends up level. It is a lot easier if you don't bother and just let the deck slope. This way you can use 2x4's on edge for joists and make panels about 6'x6' square (or whatever size might work best for your deck). The band joist, or header piece that joins the joists has to be narrower and held up to the top edge of the joists to let the rain pass through underneath. maybe use a 2x3 for your "band joist. I purchase rubberized padding material from my rubber roofer that is about 3/8" thick that they use under the membrane, cut it into 2" wide strips and use roofing nails to attach it to the undersides of the joists as padding so that you don't wear holes in the membrane. Really pound the roofing nails in so they compress the rubber and become countersunk so they won't pose a danger to your membrane. This padding also prevents your floating sections from moving around much b/c it sort of grips the rubber roof. Generally I use screws for all of my connections with the panel framing and for the deck boards. I like mohogany 1x decking with slightly rounded edges, but any decking can be used; use screws for strength and rigidity of your floating panels. Make sure to take great pains to protect your roof while you are working up there. Get 1/2" plywood spread over a big enough area to work on and immediately pick up any dropped nails or screws before they get under the plywood or someone steps on one, thats all it takes to make a leak. Construct your panels on sawhorses to further minimize the chance of sending a screw or tool through the membrane. Don't drop your hammer on the roof either as this may cause a hole. I am always wary that any preservative or stain not drip on to the rubber roof as it may react with it or weaken it.
Next time I have one of these roofs to install I am going to do it myself with fiberglass instead of subbing it out and worrying about punctures. See: http://www.renovateyourworld.com/wwwboard/messages/28457.html
Remember that you need railings if you don't have them already, and there are strict code requirements for these. I usually build the posts right into the structure of the house and have my roof guys bring the rubber roof a ways up each one.