Clio supports the ability to apply discounts to individual line items (Time and Expense Entries) as well as to the entire bill either on a percent or dollar-value basis for those bills in the Draft or Pending Approval states. You will see the "Edit" option next to the "View" option from your list of invoices.
You can also move into the draft bill you would like to modify and click on "Actions" at the upper right followed by "Edit" from the drop-down.
When you are in the Edit page of the bill, you can apply any discounts you would like to individual line items in either percent (%) or dollar ($) amount. You will see this option under the "Discount" column. For discounts to be applied on the entire bill, go to the "Invoice Discount" section below the subtotal of your invoice to apply either a percentage or dollar discount. You can also add notes about the Invoice Discount in the "Discount Note" field. Once you save the bill, the discounts will be applied:
Discounts of over 100%
The bill will show a negative amount.
The negative balance will not be registered automatically to your accounts. The amount remaining that should show as belonging to the client needs to be manually entered into either the Account tab or the Transactions tab within the matter. Select the correct account you will have the overpayment stored in, and make a note that it is the overpayment from bill [#] for future reference.
To learn more, click here to learn how to create transactions in Clio.