A few thoughts...
You can record and use several outcomes ('responses') in the same experiment. For example, you might measure peak height, peak separation, and so on.
JMP calls your HPLC parameters 'factors.' All of yours may be included in a Custom Design. I strongly suggest entering them as continuous factors, even if you are thinking about only a few levels. Also, considering using the widest possible range for each factor to elicit the larges possible effect. This practice dramatically increases the power of your statistical tests and gives you the most stable, precise estimates of the model parameters..
Define a model that includes terms for all of the possible effects: first-order or 'main' effects, interaction effects, and non-linear effects ('powers').
The Prediction Profiler will allow you to evaluate parameter settings once you select your model and fit the data.