When recording an Invoice as Paid, you will have to record the payment type in addition to any comments about the Payment. To set up these payment types: 

Click on the menu at the top left corner of the page and go to Fields under Settings and Tools:

Select Payment Types from the left hand side then click the +Add button:

Enter the Payment Type and whether you'd like it to be active:

Then Save

The Payment Type will now appear in your list under Fields and if Active, in the drop-down when you mark an invoice as paid:

If a Payment Type is Inactive, the green tick box will be greyed out, and the payment type won't appear as an option when you record a payment:

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