Bank reconciliation — the statement and the books, line by line
Import the bank's statement, let the rules match it to the books, finish the rest by hand, and read the reconciliation statement: books, plus what the bank has not seen, less what the books have not seen, equals the bank.
Menu → Bank → Statement. Download the statement from the bank's portal (CSV or Excel), pick the account and the bank's column map, and import. Lines already on the account are not taken twice.
Auto-match runs the rules in order: a payment's UTR, a deposit slip, a transfer's reference, a challan number, a deposited cheque's number (which then *clears*), a company's receipt by its UTR (which is then marked *banked* on the receipt); then the one book line of the same amount within three days; then the narration — a bank charge is posted to *Bank charges* and interest to *Interest received*, by patterns you can edit.
What is left is the workbench: *Match…* it to one or more book lines (a bulk NEFT the bank shows as one debit against five payments; three NEFTs against the night's one collections line), *Post…* it to a named account, or *Exclude* it with a reason. *Unmatch* undoes a match.
The reconciliation statement (Reports → Bank reconciliation, and on the tab) as at a date: balance per the books; add deposits the bank has not credited; less payments the bank has not debited; add and less the statement lines the books have not seen; excluded lines; balance per the bank; difference — which should be nothing, and if not, is the number to explain.