Set up non-deductible amounts for each installment when creating a pledge schedule so that when the payment is created (manually or by auto-processing) the non-deductible amount can be filled in automatically.
This could help:
Alert someone who is manually entering the payment that not all of it is expected to be tax deductible
Fill in the non-deductible amount when a payment is autoprocessed so that the payment doesn't have to be manually updated.