Safety first! Regardless of which configuration you decide on, always use a new pair of batteries, and keep them married. Mixing batteries of different brand, age, and capacity can be disastrous, especially in a series configuration. Both batteries in either configuration MUST be capable of delivering the required current simultaneously, if one battery cannot keep up, a thermal runaway may result in a battery venting and explosion. You don’t want to be “that guy” right? We don’t either.
Even with new, married batteries, the CDR of your batteries is another critical factor. Bear in mind that with a series mod, you will be limited to the CDR of a single battery while theoretically you can double that with a parallel mod.
Please read our series of articles on battery safety for an in-depth understanding of batteries and their limitations
Warnings aside, if you are a low wattage vaper who mainly uses single-wire coils and you are looking for longer run-time, consider the parallel mod. It will also give you more headroom by providing higher current limits.
If you prefer vaping at Mach 1 with your hair on fire (Maverick) while chucking some serious clouds, the higher-voltage series mod provides the necessary muscle. A series mod will easily drive larger wire mass, and ramp more quickly, while providing blazingly hot vapor — this mod dares you to tame it, just be mindful of your battery limits.
Whichever you choose, be safe and have fun.