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If you know you will always have exactly two entries in the paymentCalculations array, you can use an Expression Evaluator to add them. Set the Field Expression to:

${record:value('/paymentCalculations[0]/netPay') + record:value('/paymentCalculations[1]/netPay')}

If there are a variable number of entries, you will need to do this in a script evaluator. For example, in Jython, it would be:

for record in records:
    # Loop through paymentCalculations array, summing the values
    # into totalNetPay
    totalNetPay = 0
    for pay in record.value['paymentCalculations']:
      totalNetPay += pay['netPay']

    # Set the totalNetPay field in the record
    record.value['totalNetPay'] = totalNetPay

    # Write record to processor output

  except Exception as e:
    # Send record to error
    error.write(record, str(e))