I have some information about linking paid invoices to a project. You'll need to create the invoices from the project page, or create it to link the transaction. Thus, adding the paid invoices to the project is unavailable.
To add it on the project page:
Go to the Projects menu, then tick the project name.
In the project page, click the Add to project drop-down and choose Invoice.
Enter the invoice details. The, hit Save and close.
To create an invoice outside of the project page:
Go to +New at the top, then select Invoice.
Choose the project name from the Customer drop-down.
Enter the invoice details. Then, click Save and close. See the attached image below.
For more information about projects, check out these guides: