think that's a very cool idea, congratulations !
Acoustically there shouldn't be any problems or any significant difference two stacking two B1's on the side. As a rule of thumb, as long as the acoustic centers (and the follow) are closer as a quarter wave length at the highest frequency of interest, the exact location doesn't make much difference. For the B1 that comes out to 16" or thereabouts so your ingenious setup should work great.
To take the questions in detail
a) a 12" separation of two B1s;
As pointed out above that will not result in a significant difference.
b) not having the B1s on the floor;
In the extreme case, that would loose 6 dB, which is a fairly sizeable difference. "Extreme" in this case means that the B1s are somehow suspended in free air with no reflecting surface nearby, but that's a fairly unrealistic scenario. Lifting the B1 by a few inches doesn't really make much of a difference.
However, wall-loading does make a difference. We assume that the "normal" case is on the floor (within a few inches) and relatively close to one wall (within a couple of feet), either a side wall or a rear wall. If you are far away from any wall, you will have to turn up the bass a little and if you are in a corner you may have to turn it down somewhat.
moving the B1s into a corner will gain you up to 6 dB more bass.
c) not stacking the B1s on top of each other?
Again, no problems as long as they are not too far apart (16" or less).
Please be aware that the 16" is not some magical hard number. If the B1's are further apart you may experience some power loss or interference at a few spots in the audience, but nothing drastic. Only at about 6 feet or up you'll find that the overall radiate power has dropped by 3 dB, which is certainly noticebale but not a dramatic change either.
Hope that helps