ledger and bay door

Yes drop the ledger, and place it under the bay, drop it so you'll get air. I imagine the door will end up with a 1" to 1 1/2" drop to the final decking.

Flash it correctly though, and dependent on your siding on using a spacer or not (either treated wood spacers or extra washers on the bolts) to minimize the connection of wood to wood without venting (air)

For bolting the ledger to the house have a look at the 2nd chart down on the bolting schedule of my deck site, deck connections page I think it is. Then to the beam and joist span charts to figure where to place the beams.

http://www.altereagle.com/

http://decks-ca.com

http://kingofcrown.com

Alter Eagle Construction & Design