The Reference Number field is an alpha-numeric free-text field. When selecting Patient Payment Check or New Insurance Payment from the Payments menu, the Reference Number field will be labeled "Check No." and can be used to document the check number for your internal tracking purposes. When a non-check type of payment is selected, the field will be labeled "Reference No." and can be used to document additional information about the payment. "VISA1234" could be used for a Credit Card payment type to document the type of card and the last four digits on the credit card, for instance. This is one common example, but you can use the Reference Number field in a way that fits the needs of your office.
The Reference Number field may be located before or after the Amount field in the Payment Window, depending on your settings in Preferences.