SoM is correct that the "alternate" B speaker setup won't get Audyssey calibration, so in a perfect world you'd really just want to have your two best speakers as your primary L/R mains for both movies and music...
But to answer the question, yes you can absolutely use your subwoofer with the "B" speakers.
First, you actually don't have to give up the "wide" speakers to accomodate a separate 2ch setup. There are several different Amp Assign modes that will accommodate this configuration, you should really study the amp assign explanation on pg 100 of the manual, as well as the flow chart on pg 140 and the speaker output charts starting on pg 177:
1. The option you noted, "7.1ch + Front B"
amp assign, is the standard mode which dedicates 7 amps to main zone and 2 amps to the Front B speakers. You then dictate which pair of speaker posts will output the Front B audio by selecting the two pairs of speakers which you still want to use in main zone using the "Main Speakers" menu which follows the Amp Assign setting (clip from pg 100 in the manual):
So for example if you select "F.Height/F.Wide" from this menu, then by extension the S.Back amps will output the Front B signal. Note that with this setting, even though you can connect up to 9 channels in Main Zone, only 7 can be active at a time because only 7 amps are assigned to Main Zone. When you select this Amp Assign mode, you will also have to go to the "Front Speaker" setup menu (pg 145) and designate which of the A or B (or A+B) front speakers is used for multich vs. 2ch playback.
- Alternately, you can choose the "7.1ch / 2ch Front(Bi-Amp)"
setting, which dedicates four speaker terminals to the Front B speakers. In this setting, your Main Zone is locked in to the standard 7.1 configuration (5.1+S.Back) and you would bi-amp the Front B speakers using the Front Height and Front Wide speaker posts. When in normal (multich) operation, the system operates as a standard 7.1 setup. When you switch to Front B speakers for 2ch playback, the two amps dedicated to S.Back switch to the Front B speakers so now there are four total amp channels allowing for 2ch bi-amp.
- Finally, you can choose the "9.1ch/2ch Front"
setting. With this setting, you again use that "Main Speakers" menu above to determine which four extra channels are active in Main Zone, and by extension which two speaker posts will be powering the Front B speakers. This mode is basically the same as "7.1ch + Front B" but allows you to run 9 channels simultaneously in main zone. With both this and the 2ch bi-amp mode above, you don't need to use the "Front Speaker" setup menu because 2ch playback is pre-configured to lock in to the "B" speakers. So when you enter a 2ch playback mode, the switch happens automatically and two of the amps dedicated to Main Zone switch automatically to the 2ch speakers.
In all of the above situations, you can use the dedicated "2ch Playback" menu (pg 145, under Speakers>Manual Setup in the GUI) to designate your settings for 2ch playback. In this menu, you switch the setting to "Manual" which disconnects the 2ch settings from the main settings. You can then set up independent distances and levels for your "B" speakers, but more importantly you CAN set up bass management as well, so the subs will indeed be in play if you so choose. You can either set the speakers to SMALL with a crossover, or leave them LARGE with the sub set to LFE+MAIN if you want double bass for stereo playback. Note that if you go with LARGE/LFE+MAIN in this menu, the "crossover" frequency becomes the LPF for the double bass signal going to the sub.
Finally, although it is somewhat unorthodox, you can even use Audyssey correction for the subwoofer and also use Dynamic EQ for 2ch playback by setting the EQ mode to "Audyssey Bypass L/R". In this EQ mode the filter correction is applied to all speakers EXCEPT the Front L/R mains. So you could for example set the speakers to SMALL/80Hz, and the <80Hz information would be crossed over to the subwoofer and have Audyssey XT32 EQ filters applied, whereas no EQ would be applied to the "B" speakers above 80Hz (which you wouldn't want, since the FR/FL filters were calculated for your "A" speakers).