The two battery option is more reliable for most folk - connecting one battery to two devices can lead to some interesting interactions when a bit of wire falls off, the options are fewer with two batteries. If you have confidence in your competence, go for it.
Two batteries can only be charged together if they are known to be in an identical state of discharge and condition. The lower charged one will try to charge itself from the less discharged one until things even out. The safe(ish) way is to charge each through a diode such as a 1N4005. If the pair is offered 800mA, then the lowest will charge at that rate, hogging the juice, then they will both share alike when parity is reached.
Best solution, if possible, change the motor to a 12volt one. OR, fit a resistor in series to calm it down a bit. (An element from a dead heating device such as an electric fire or hair dryer is good - find the best length for your purposes, and connect via a pair of screw terms. OR cross your fingers and hope you don't forget and shove that stick too far, too often. Thruster motors, by tradition, are very well hidden.