With a Voc of 49.6V, you should forget completely about getting a cheaper 40A controller with a 100V limit. Just two panels in series would be too close to 100V to measure, and a single frosty morning will bump up the voltage significantly past 100V.
With 12 panels, I'd wire them in series to get 3S4P. Running at 123Vmp will duplicate what I am running right now, but you'll need a 200V controller for that. I have a Midnight200 controllers, though you might also want to look at Epever's 8420AN, or 10420AN.
Wired 3S, one string will be producing a theoretical maximum of 440W X 3 panels/25V charging =52.8A. I wouldn't expect ever seeing more than 90% of nameplate, so call that 47-48A. So, one 10420 controller could handle two strings.
At these power levels, you might seriously reconsider switching to 48V. That would cut your amperage values in half while maintaining the same power levels. (440W X 12 panels)/50Vcharging = 105.6A max (90A in the real-world).
I see you have 12V batteries. If you get two more of them, you can wire them into a 4S2P battery bank. What's the amphour capacity of them? Assuming they are 100Ah, and they would like to be charged 1/8thC, then you'd get (100Ah X 2 strings)/8 =25A. Even expecting only 85% of nameplate output, you only need (25A X 50V charging)/85% = 1470W of panels. So, this means your battery bank is too small for the power levels you are talking about. Only one of the 3S strings would be enough to keep that battery charged.
So, this looks like it's shaping up into a poorly designed system, with far too small battery and far too large solar input. I'd stop buying stuff now, and wait till you have a more concrete plan on creating a top rate system. BTW, you haven't even mentioned yet what it is you want to power. An itemized list of what you want to run should have been the first thing you did, and then design from there.
