I am fairly novice to this stuff so I will define the situation. Please share your thoughts on the situation.
I have two factors (Inputs A,
that individually and directly affect factors C and D (Measurements). Increasing either A, or B leads to an increase in C and D. The issue is that currently, I am trying to decouple the benefits of A and B from C and D. I attempted an RSM DOE where I left C and D as uncontrolled factors. JMP added a few more runs and my hope was I would get enough variation in these for the model to generate appropriately. Unfortunately, after filling in the factors with the C and D measurements, I evaluated the design and got this variance profile. So I believe I was unsuccessful in this attempt.

How does one model factors that are directly influenced by other factors?