First please identify your panels as to their specs ie, Isc, Voc, wattage Vmp, Imp if you have that but don't need it.
Second, how are they (how many) connected for series or parallel or both?
This will clear up whether you have the right controller.
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EDIT--OP says two 100w panels. to get 44 volts output that means they are in series. Wrong! they should be in parallel. Now voltage will be 22v and your amps will be 12 instead of just 6. That will help :)
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To get better charging for your T-1275, I recommend the adjustable voltage PowerMax and use it as a portable charger, leaving the WFCO in place for when on shore power. That saves you from a bunch of wiring work.
https://www.boatandrvaccessories.com/products/powermax-pm3-60lk-12-volts-60-amp-power-converter-battery-charger-w-led-lightThis is not the same charger, but use it like this when off grid: