On your overview page in the BAFA portal, you have three icons under "Aktionen." When you hover the mouse over the middle one, the description appears ("Dokumente zum Antrag hochladen"). There you can upload your invoices. I took care of that at the same time as submitting the proof of use. If something is missing, it will certainly waste time again because BAFA will first send you a letter asking you to submit or upload the corresponding invoices. Apparently, it is no longer possible by mail. I had to submit the documents digitally (which makes sense).
However, none of this is user-friendly. It also took me a while to get the hang of it.