The problem with a parallel set up is that one battery will tend to deliver the current over the other and worse since no two batteries are the same one might actually discharge the other. If you do go this route link the batteries +ve to +ve and -ve to -ve but make sure that you take your load positive from the one battery and the negative from the other. If you have two batteries of the same make and age as well as having a constant float charge this probably won't amount to a problem.
The advantages of using the batteries in series is that it is in essence just making the battery bigger by combining cells in series. I've also been told that 6v batteries tend to have thicker plates and therefore last longer but thats just what I've been told, probably an american thing derived from golf carts or something. But isie is right in that if one battery goes at least you have a backup whereas if one battery goes in a series connection you are out of the game until you replace it.
Just remember that the 2x105 12V @ 12V = 210ah or 2520Wh or R15.23 per ah (1600*2/210)
2x122ah 6V @ 12V = 122ah or 1464Wh or R18.03 per ah (1100*2/122)
So it may be slightly more expensive to buy the 12v once off but you're actually saving per amp hour.
BTW, where are you getting your batteries and what type are they? Battery centre sells deep cycle silver calcium 105ah batteries for just under R1.5k.
Lastly just make sure that your DC side of the inverter (the battery links and the load connection) has decent size cables and you keep them as short as possible since it is a 12V system. Using 3000W on 12V equates to drawing 250 Amps through those cables. Even with thick cables, make sure they aren't heating up too much. To give you and idea, if you geyser is 2200W (pretty typical size) its only drawing 10amps when in use so 250 amps is not a small amount of current.
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