9V from two AAA batteries plus charge pump: batteries in series or parallel?
As a rule of thumb, the closer your input and output voltages of smps's the more efficient it will be. With a Dickson, that rule is the same as you've got diode (or mosfet) voltage drops to overcome. And you'll need more stages to get to higher voltage with a 1.5V input. With 3V you have less stages and therefore less voltage drops wasting your energy.