Hi Nathan,
I assume that "PV+ES" means PV with energy storage (battery). When you specify the ITC as a percentage, SAM calculates the percentage based on the total installed cost, regardless of how the battery is charged and discharged.
You can verify this by looking on the Results page Cash Flow tab at the State ITC and Federal ITC rows (under "STATE INCOME TAX" and "FEDERAL INCOME TAX", respectively). The ITC amount should be the product of the percentage you specify on the Incentives page and the total installed cost on the System Costs page (plus a fixed ITC amount if you specify it on the Incentives page).
Best regards,
Paul.