For an imaging system, the overall wavefront error is defined to be the difference between the actual wavefront in the exit pupil and the reference sphere (note: the location of the exit pupil relative to the image plane can be found in Analyze -> Reports -> System Data).

I think what you may be asking about is simply fitting a measured surface wavefront error with Zernike polynomials for use in OpticStudio (this is the error in the surface shape relative to the nominal design target, typically measured in waves).  That can be done using third-party software (e.g., Matlab).  Attached are a few pages from a reference that describes the fitting process (Numerical Simulation of Optical Wave Propagation, by J. Schmidt); it may be helpful.  You can then enter the coefficient values into the Zernike Standard Phase surface for simulation.