When to use a manual payment
You might occasionally want to pay an invoice with a handwritten check, rather than a system-generated check. For example, you might want to write out a check to someone who has shown up at your office with a COD delivery. Even though the payment isn't being generated by the system, you will still want to record the invoice and payment for your record keeping.
Manual payments are not the only way to produce a single payment. An alternative is to specify an invoice and flag it for immediate payment. The Pay Immediately field is on the Payment tab of Basic Invoice (AP20.1) and Taxed Invoice (AP20.2). The Pay Immediately field is also on Payment Schedule Adjustment (AP30.1). Then run the pay cycle to produce the check and close the cycle.