The way the Flux is wired, it puts whatever is connected to the esc in series. To run lipos in series, they can be diff cell counts, but they have to be the same capacity and should be about the same C rating and have about the same number of cycles. Ideally, they should even be same brand.
You can't mix a 5300mah 2S and a 3000mah 3S.
I run a 2S 5000mah 25C and a 3S 5000mah 25C pair in my Flux, its my fav, like the way it runs.