First, run the Unapplied Transactions Report in Financial Reports v3 in the Reports Page. This will allow you to view permits that have unapplied fees. If they are unapplied due to an error, they can be corrected. If they are unapplied due to the fact that they are a credit or may be transferred to another permit, you will be able to make note of that.
Second, run the Revenue Exceptions Report. This is important, as exceptional payment types do not show up in the surcharge report. Reconcile the Unapplied Transactions and Revenue Exceptions Reports.
Third, run the State Surcharge v3 Report. If this report does not match your accounting, run the State Surcharge Details v3 Report to find the records that are creating the discrepancy.