If your client has already paid a deposit fee, then it is best to mention this somewhere on your invoice, when creating or reissuing a new invoice for the remaining amount. You can do this either within the description, or within the additional 'comments' section.
See examples below, for reference:
Below are examples of what both methods would look like in the final invoice. On the left: if included within an item description. On the right: if included within the additional comments section.