torch down roof.
The deck rests on the roof. I would avoid a ledger because you're asking for trouble with leaks. If you do go with a ledger make sure you silicone all the bolts. Don't penetrate the EPDM at all. If you do go with the ledger put washers behind it so there is room for drainage.
As far as flashing, I would put it under the door, but it's hard to imagine the layout you might have and where and if it would be beneficial.
Distribute weight with horizontal boards on the roof.
Make the deck so it can come apart with screws and removable panels to get to the roof if needed.
Make sure you have the wood waterproof.

http://www.metacrylics.com/application/
I never used this stuff so can't vouch for it but check it out.
Also, being it's so low it will be alot of moisture for the wood. This company makes a product to prevent joist rot.
P.S. This project must be done right so I would definitely consult with a local contractor for advise and building codes as to what is good for your local area.

http://www.graceathome.com/pages/decking.htm
forgot the link for the joist protector stuff.. never used it but since you will be low with moisture.. and have no plans to remove this thing for repair.. you might want to consider this stuff or stuff like it to aid you for the long haul.

A torch down modified makes a good roof,I woudent go the glue down,lay the stringers flat not on edge,Like the Gorilla says do not put any holes in the roof. Flash under the door melt the roofing to the flashing. I always have my roofer guy place a cant strip all around the house side. John

Thank you both for your replies! One question about the stringers, though. How would I compensate for the slope of the roof if I lay them flat? The deck extends 8 feet from the house, so that means a 2" drop.

here's a link that may be useful.

Here is a link that might be useful: sleeper tips

another link where they discuss it.. read the whole thing.. it's question/theory, answers..etc
You'll have a few techniques to consider.

here's another link to a rooftop deck on bob villa.. It has video around 3 minutes long... the last 30 seconds shows you a technique they used with sleepers.
http://www.bobvila.com/BVTV/HomeAgain/Video-1411-04-0.html

Here is a link that might be useful: some sleeper tips

2'' fall in 8' with a torch down is way too much,in 8' 1/2'' is fine. landing the stringers on edge is just asking for trouble the weight is not spread out enough,just for a little more protection I have Rick the Roofer leave me enough material for buffer strips of the modified and I lay them under the stringers granulated up. J

This forum topic is a small but subtle reminder on why I hire a contractor to do some things like roofing. I can install deck drainaige systems under my 2nd story deck but that's because I'm in the shade when doing it, roofing is hot work.... to hot for me

Here is a link that might be useful: Deck Drainage system