Multiple batteries, aka battery packs, are better rated in watt hours than mAh.
Dual 3Ah (3000 mAh) batteries in series output an average of 7.4V and rate 3 Ah.
Watt hours = V * Ah = 7.4 * 3 = 22.2 Wh
Dual 3Ah (3000 mAh) batteries in parallel output an average of 3.7V and rate 6 Ah.
3.7 * 6 = 22.2 Wh
Both circuits will output 22.2 watts for an hour, or 11.1 watts for 2 hours, etc. Individual battery amp draw is the same in series and parallel at the same regulator power output and maximum regulator watt output is also the same with the following caveat.
Regulation efficiency is a little different for each of these circuits, but that is due to the regulator chip, not the battery circuit. Regulator efficiency also changes with different watt outputs or coil(s) resistance values using the same mod, batteries and the same circuit.
So, for all intents, it really doesn't matter if the mod is wired in series or parallel