Dear Jen,
If all of the modules are in the same orientation, and the module string length for each MPPT input on the inverter is the same, then SAM's single MPPT input model will work fine to represent an inverter with multiple MPPT inputs.
When you model the array using multiple subarrays, you can assign different tilt and azimuth angles to each subarray (or combine subarrays with fixed arrays and trackers). The only limitation is that SAM requires all subarrays to have the same number of modules per string (and type of module), and models the inverter as if all subarrays were connected to a single inverter. In that case, SAM estimates the effect of voltage mismatch between the subarrays.
You are correct that SAM models shading of the array by nearby objects as a reduction of the beam irradiance incident on the array.
Best regards,
Paul.