Other guys are a lot more experienced/qualified than me for this, but I'd have thought if the room was a bit light on the bass, putting Monitor B in is more likely to result in recordings that are bass-heavy?
Anyway, I'd choose on the ones I "preferred". Back in my studio (living room in my case - no chance of accoustic treatment or anything along those lines) I tend to get round the "reference" bit like this:
All my stuff goes through a mixing desk - my amp modellers, synths, drum machines, the family CD player, the output from my laptop/souncard, the DVD player, and so on. And they all use my (cheap!) powered studio monitors.
About the only channel on the desk that ever has any EQ set at all is the channel that takes output from my laptop/soundcard - and I "calibrate" that by disconnecting the laptop, connecting the CD player to the same channel and listening to music similar to what I'm about to play around with. I set the EQ so that I like what I'm listening to (still the CD), then I disconnect the CD player, reconnect the laptop, keeping that EQ on the channel. Then when I listen to my playbacks and mixes, I know I'm in the right ballpark if, using this EQ on the desk, I like what I'm listening to.
Until I figured out this way of doing it, my recordings were either tinny or bass heavy, pretty much hit or miss, but recent attempts have been a lot more satisfying :D