As the others have stated, capacity is capacity, doesn't matter if the batteries are in series or parallel. There are a few other considerations though.
First off, let's look at your question, 12V batteries (or 24V for that matter) are not a constant 12V output, so you'll most likely need 2 DC-DCs for 2 stable voltage rails. Let's look at which configuration is better. Assuming 1Ah packs for simplicity.
In parallel, with perfect current sharing you'd have 12Vin, and either 12Vout or 24Vout. Power In = Power Out, so 12(Iin12) = 12(Iout12) + 24(Iout24). With a parallel configuration, each pack will see half of Iin drawn from it. If we then go to a series configuration, with the same setup the equation changes slightly: 24(Iin24) = 12(Iout12) + 24(Iout24). In this case, each battery sees the same current through it (Iin24). If the 12V and 24V output currents stay the same in each configuration, we have 12(Iin12) = 24(Iin24) so Iin12 = 2*Iin24. Since each pack sees half the current in the parallel configuration, the current drawn from the packs is the same regardless.
So does it matter? Not in the sense that one configuration will provide more capacity than the other. What you'll have to worry about with either configuration is how you balance the cells. Parallel and series connections each have their own pros and cons for balancing. In parallel you're guaranteed an equivalent voltage on each cell, but it can be tricky when they start to age and sink/source current at different rates. Similarly for series connections they will always sink/source the same current, but their voltages will increase at different rates. I personally find series connections to be easier to balance, and there are a lot of ICs available that do it that way as well.