Stryker, I'm not sure I'm understanding what you're saying, but if you mean having two voltage multiplier stages running in inverse phase, yes that would be possible. You could keep the first stage(s) separate and feed them an inverse phase square wave, and then in the final stage, the diode would be connected to the same capacitor. You could it even generalize it and run x stages at 360/x degree phase.
Is it worth it, that's another question. If you can't get enough juice or a clean enough voltage out of this circuit, then you probably need a whole other voltage boosting solution anyway, like a proper DC/DC converter with an inductive element.