Hi Noah,
If you model a PV system with the Flat Plate PV model that has two subarrays, SAM assumes that each subarray operates at its maximum power point, and that both subarrays are connected to the same inverter or bank of inverters. That should accurately represent the scenario you describe. If you provide a separate shading scene for each subarray, SAM will adjust each subarray's incident radiation to account for losses due to shading.
Best regards,
Paul.