Doing dual input control systems is a PITA. Actually building it isn't really an issue but tuning and making it stable is. The simplest set-up is have it set-up such that you are essentially using the temperature difference between the two probes but that only works for certain applications.
Can you give me a pretty good decription of what you are trying to accomplish? I need to know what is part of the system that you are trying to control (like size and number of tanks, where your heating elements are located, how you are moving the flow about, etc). I'll try me best to draw up the most stable configuration for you.
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