Currently I'm working on diabetes. I want to generate mathematical models of the enzymatic response of the glucokinase enzyme in the presence of allosteric molecules. I want to understand the basic strategy behind the mathematical model building of such phenomena.
You could look into flux-balance analysis of metabolic pathways.
I think a general strategy would be to propose a model (maybe a qualitative model about how things work), then collect some data, and use the data to try to train your model to be quantitative - try to put equations on each of the interactions, and estimate the parameters of the equations - and also keep some of the data back, and use it to test the performance of the model.
Maybe you find some clues in Chapter 7 of L.v. Bertalanffy's book "General System Theory" (New York: George Brasiller, 1995).
If you want to model the time course of your processes the technique could probably be compartmental modelling (compare with pharmacokinetics and pharmacodynamics ) . There should be lot's of sources available on that topics. Then proceed like Jonathan suggested.
As regards allosteric regulation, I recommend the classic by Monod, Wyman and Changeux, On the nature of allosteric transitions. J Mol Biol. 12:88-118, 1965. It is an excellent paper using mathematics to deduce experimentally testable hypotheses. On enzyme kinetic problems, there is a large literature from the 60s and 70s that people are not aware of as much anymore (see books by Irwin Segel, Enzyme kinetics, or Cornish-Bowden). Generally, using mathematics means that numbers play a role in the question you ask.
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