Generally you would only develop a model if (as in your case), you have something that you want to control. In that case, you should start by:
- List the outputs that you want to control.
- List the inputs that you can modulate.
In your case, you want to control chamber temperature and object temperature. You can modulate the chamber heater and the object heater. Now, you have to ask yourself:
- How do the inputs affect the outputs? You should shoot for an equation in the form of $\mbox{[outputs] = f(inputs)}$
This is important because you generally only want to model the things that are pertinent to the task at hand.
For example, say you want to develop cruise control for a car. The output you want to control is vehicle speed and the input you can modulate is throttle position. Can you model coolant reservoir level? Sure, but you can also assume the coolant system is functioning normally. Can you model the internals of an automatic transmission? Sure, but you can also assume that the automatic transmission gives output power equal to input power minus some losses.
The point is, you have to make some set of assumptions about the "nominal" scenario. Once you have your initial model, you attempt to validate the model by getting test data. Typically this means feeding an actual system a particular set of inputs and recording the response, then feeding the same inputs to your model and recording the response. The results should be (very close to) the same. How close is "good enough" depends on your application, and could be anywhere from "it generally trends the same" to virtually no error.
You can try developing a rudimentary controller around an unvalidated model if you've got time to kill, but you should generally wait for validation before expending a lot of effort on the controller because math errors and faulty assumptions can cause you to have to start over with controller development.
You can also skip the mathematical description if the system is too complex to be described mathematically, or if doing so would take too much time. "Empirical modelling" runs a similar sort of tests you would use to validate a model, but with the concept that, by seeing how a particular set of inputs create an output, you can derive some pattern that you can extrapolate a model that gives outputs for other inputs.
In your case, if you're really concerned with better control, I would probably suggest trying to build an empirical model. Try a variety of inputs on only one heater and record how that impacts chamber and object temperatures. Then do the same on the other heater. Best case is the effect of each heater is decoupled or weakly correlated to the other temperature - the space heater only heats the space and the object heater only heats the object. In that scenario you can have independent control, though I would imagine this would probably only happen if you had significant chamber losses relative to the output of the object heater and/or the chamber had a large thermal mass relative to the object.
And on a final note, I'll just add that, when gathering test data for a particular model, you should try varying all of the "nominal" conditions that you assumed to make sure it doesn't have an effect you should be modelling. For you, that would probably mean checking the ambient air temperature around the chamber is varied through all of the expected conditions. As I mention above you're probably more likely to achieve independent temperature control with large chamber losses (because your heaters are not bi-directional; they only make heat and cannot remove it), and the chamber losses are going to be related to ambient temperature. Testing in only hot weather (or vice-versa) will skew your results, model, and thus controller to a point that it might not be useful when the weather changes.