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How do you reconcile a payment run to the bank and the ledger?

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Answer

After a run, agree the total of the bank payment file to the AP clearing postings and to the cash leaving the bank account. Investigate rejected/returned payments (e.g., closed accounts), re-issue as needed, and ensure each cleared item matches an open payable now cleared. This ties the sub-ledger, GL, and bank together.
Real-world example Two ACH payments bounce due to closed accounts; AP re-opens the payables, corrects bank details, and re-pays in the next run.

Common follow-ups: What causes returned payments? | How are rejects re-processed?