I would imagine it would work pretty well, however, I honestly don't think it would be worth the extra effort. In my experience with automotive electrical, which involves mostly car audio equipment, I don't think the added pull off the alternator is really costing you much in the way of fuel mileage. I've run audio systems that pulled in excess of 100 amps, and had no real reduction in mileage. Only problem I have ever encountered was the usual dimming of the lights during big bass notes at excessively high volume. More often than not, this was corrected by adding 0 gauge wires to the electrical system at key points. Battery to ground, alternator to battery, and block to ground. In the audio world, this is referred to as the "big-3" upgrade, and it works wonders on your electrical system by making it run more efficiently. Of course, for the HUGE systems, we would upgrade to a HO alternator, and upgrade all the wiring, major PITA! I'd venture to say that even if you don't run a full tilt stereo system in your car, doing the big-3 would greatly diminish the strain on your electrical system caused by your HHO generator.
In relation to your particular case, if you can actually hear the difference when your generator comes on, I would HIGHLY suggest doing the Big-3 and see if the problem goes away. You don't even have to spring for 0 gauge wire, 4 gauge will work just as well. If you need a supplier for cheap 4 gauge, go to http://www.knukonceptz.com
as they have the cheapest prices I have ever seen, and the quality is top notch (I use it in all of my installs).