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Like other daily operations, to pay supplier's bills the best solution is to have the computer print the checks, as this process marks the bills immediately as having been paid and prevents the double paying of bills.
The bills are recorded with a bill payment due date. Then, on a regular basis you can run the "Check Run ,Bills Due" report which looks at the payment date, check to see if it's been paid yet, and if not, recommends that it be paid. Optionally, this report can also create Unposted checks and place them in a batch of checks to be printed and posted at a later date.
If you manually write a check, it should be entered into the computer immediately, preferably before the check is given or mailed to the supplier.
To pay supplier bills see How to Pay Supplier Bills.