I assume you've got at least four 6v batteries? - if you just had 2 you wouldn't have any choice.
if they're similar age and same type it probably doesn't matter too much; if not, and they are flooded types, I would probably connect them for 12.5v, rather than have a 12.4 parallel with 12.6, to minimise cross charging between them.
If they're sealed types and you have a substantial charge source, then you might prefer to live with the cross charging and put the batteries in matched pairs - or: put them in 12.5v pairs as above, but you may then want to consider using separate shunt regulators for each half of the final battery - if you have one reg for the full 12v you may find one half of the battery goes overvoltage and one under when charging - not good for sealed batteries.
mab