Hello,
I do not have specific advice on how to change the system losses in PVWatts for different system designs. You can find some discussion of the default loss values in SAM's Help topic on the PVWatts system design page. The losses are generally appropriate for a rooftop system.
You might also want to do some parametric studies to see how much of an impact the losses have on your output metric of interest. For example, if you are interested in the project net present value (NPV), you could run a few simulations to determine how much the NPV is affected by a 2% change in the wiring loss assumption.
I did a web search for "PVWatts losses" and found a few articles and white papers that might be helpful. For example, the Enphase inverter company has a technical brief on losses (or derate factors) that they consider appropriate for systems that use their inverters.
Best regards,
Paul.