I'm no electrical genius, but I just think you need to make sure that all of the flexwatt that you are hooking up to each input of the herpstat is the same length.
I think you said you would be using 1 and 2 ft pieces of flexwatt -- so just make sure that all of the 1 ft. pieces are controlled with one input, and all of the 2 ft. are controlled with the other. I think otherwise you will get two different temps -- I could be completely wrong, but maybe something to look into a little closer.
Later,
George