You don't Reconcile it, as such.
You run reports and verify if that matches your understanding of your reality, and then you address anomalies.
Negative AP = you used Pay Bills, but paid more than the bill total for that vendor. Or, someone is listing AP manually and directly on the Expenses tab of checks and credit card, completely bypassing what this Actually paid for, such as Rent or Supplies. Or, you entered bills, paid the bills, then deleted the bills, leaving AP payments.
Does any of this sound like entries that are being made?
So, you need to look at Vendor Balance Detail. Also, run
AP Aging Detail and Summary. For any row on the Summary report with a
total of 0, that also is wrong. Double-click it; you have Unlinked
Transactions.
