If I understand your question correctly, you are asking how to customie the cost (or objective) function when using a fit program in the SimBiology graphical interface. If so, then yes, you have a couple of options. I generally recommend selecting an error model that is consistent with your experimental data, and let that determine an appropriate cost function. If none of the built-in error models are appropriate, you can specify weights for the measurements either as a numeric matrix or as a function. I provided hyperlinks to the MATLAB command-line documentation, but these options should also be available in SimBiology's graphical user interface, if you create a fit program and select non-linear regression.