Bienvenidos a Panamá! Welcome to Panama.
Definitely hold off on Coiba. The currents are strong, some of the diving is blue water, it's definitely for advanced divers.
As for getting your AOW, there is only one place to go for that in Panama and it's Bocas Water Sports. Jon brings North American PADI discipline, hospitality and professionalism to Panamanian diving. Jon is a long time Master Dive Instructor, captained a live-aboard, owned a dive shop and was a long time dive instructor in the U.S. before he came to perform miracles with Bocas Water Sports. In the last two years he turned it from an operation I wouldn't go near to a very customer-focused, professional operation. In my opinion, Jon is by far the best dive operator in all of Panama.
It's a good thing you're going in September; the seas should be calm enough that you will be able to dive the wall off Bocas del Toro and Portobelo. From what I've heard, it's spectacular. For most of the year, the seas are too rough and you would have a very hard time in either Bocas or Portobelo finding a site to do the deep dive requirement for your AOW.
That said -- and Jon, forgive me for this -- my favorite diving in Panama has been at Portobelo. (My dive buddy and wife much prefers BWS, so it may be arguable.) Scubapanama is my operator of choice, there. They have very reasonably priced bungalow cabins on site that are neat and clean, and there is an excellent restaurant nearby for lunch and dinner; Los Cañones. You can also get all three meals at Scubapanama. Lunch and dinner usually include freshly caught fish and their breakfast is a great way to start the day.
Diving at Scubapanama is more expensive than BWS, but the reefs are more lush with coral and there are more fish to see.
Here is how I compare Bocas (BWS) and Portobelo (Scubapanama):
Cost of diving - BWS is much less expensive for two-tank boat dives and night dives (if they're able to do them).
Dive site locations - BWS has far more dive sites and more variety, but Portobelo has better quality and visibility. Not having dove the wall at either location, I can't judge the outer sites.
Dive operation: professionalism & customer service - BWS, no contest.
Historic location and local scenery - hands down, Portobelo.
Cost of lodging and food - definitely Portobelo. Although, Bocas has a far greater variety of restaurants, they're more expensive.
Transportation - Portobelo. You can drive there from Panama (the city) in about two hours. Unless you want to spend a 10 hour day driving each way, you'll have to fly to and from Bocas. Be sure to check with Jon about Bocas airport closures before you go.
If you'd like more info about Bocas and BWS, here's a review about my most recent trip to Bocas:
www.scubaboard.com/forums/central-america/323572-back-bocas.html
Saludos,
Grant