Given similar battery reserve power (say both with 1000mah) Which direction would be the best at maximizing runtime of 5v arduino? ie: Convert 9->5 or 3->5 ? (I searched, but I think the #'s are not a good search criteria) thanks
I think you'll find it's a toss up. If you want to look at a few concrete examples you could peruse pololu.com's voltage regulators all of which have efficiency charts included with their description.
Personally I'd go with the 3->5 because single cell LiPo are much easier to charge.
Keep in mind that a fully charged lipo will be about 4.2 volts aswell
9.6V is 3S LiFePO4, which have the advantage of being much less likely to explode. That's got to be a factor!
I assume DC-DC converters and battery protection circuitry of course.