In the on-screen menu, you can specify which speaker gets which signal. The different setup for A/B in that manual is simply a suggestion so that you can switch between A and B for different sorts of media. For example, DVD-Audio expects a speaker in the back corners for the surround and regular Dolby Digital and DTS movie tracks are recorded with the speakers to the side as an expectation. So long as you have the speakers connected to the B connections and the B speakers turned on in the menu, you're kosher.
For the sake of everyone else, here's a picture of the rear deck:
http://www.usa.denon.com/catalog/photos/AVR%203803%20Back.jpg
Here's how I would do it on my first pass (which isn't necessarily better than yours)
Front-R - Connected to Front-R
Front-L - Connected to Front-L
Center - Connected to Center
Surround R - Connected to Surround-R A
Surround L - Connected to Surround-L A
In the menu, I'd turn on only these speakers and leave the others off.
As to the rears, that depends on whether or not you're running a 7.1 or 6.1 setup.
If running a 6.1 setup, I'd connect the rear speaker to Rear Surround R. Then go into the menu and set the speakers as single back speaker and turn off the left rear channel.
If running a 7.1 setup, plug in both speakers, set the menu to 7.1 and be happy.