So, in parallel, the mAh is doubled. In theory you also split the load between both cells. In reality, it's never perfect, depending on variables such as the condition of the contact points, the condition of the cells, so on and so forth. However, the mAh is still, effectively, doubled.
In series, you're doubling the voltage of the battery is doubled, but you still have the same mAh and amp limit. You can't build as low as you normally would either because increased voltage means higher amp draw at higher resistance.
It's a zero sum game in choosing between the two if you're just using plain round wire for your builds. In parallel you have a higher mAh and, more or less, split the load of the circuit between the cells. In series you have higher voltage which means that you can't build as low, but double voltage means more power at a given resistance. The reason it doesn't really matter so long as you can adjust your build accordingly. For a given wattage, how much power the build pulls, and since we're talking about heating elements this relates to how much heat it generates, the two configurations will drain cells at about the same rates.
When making builds like claptons, twisted wires, stapled builds, et. al. it's parallel all the way because those builds generally, have so many wires run in parallel in some way or another, that the net resistance of the circuit is too low the safely or comfortable use on a series box.