If you want to charge them on Balance Charge, then you need to run them in parallel. If they are 2000mah each, then your 1c charge rate for the two would be 4 amps. If you just want to do a fast charge on them with no balance, then yes, you can wire them up in series and charge them at 2a.
I would HIGHLY suggest if you are wanting to charge more than one battery, that you get a balance board. I can tell you this, the B6AC is NOT big enough for multiple battery charging. I have some 2200's that I charge at 5 amps, but the charger can only put out about 4.3 amps max. Just on my 2200's, I need a larger 300w charger, which is 6x bigger than the B6AC. But, I"m thinking 1000w and 24v hehe. Go Big, Or Go HOME!!!