I'm not sure exactly what you are asking, so my comments may not be useful. Here are my thoughts:
1. If you are asking, can you experiment on the variables of theoretical equations to determine if those theoretical equations "work" in your specific application, the answer is yes. It doesn't matter what type of mechanism is at work, as long as you can quantify/measure the results, you can experiment on the input variables.
2. There are a number of elements you will need consider (e.g., How will you handle noise, what levels to manipulate the factors at, how many factors will you manipulate, resolution, restrictions on randomization, etc.) to determine the appropriate design strategy. I always recommend you design multiple options and compare each design for potential knowledge gained vs. resource requirements. JMP is great at creating the designs quickly.
3. Analysis is always Practical (from the eyes of the chemist) then graphical and lastly quantitative. JMP can certainly help with the analysis.
"All models are wrong, some are useful" G.E.P. Box