Hello,
Yes, I suppose you can upload the documents to the IRCC secure account. I would prefer that way, however, my PA and Spouse's application account does not list any required documents and I do not know how to upload the requested files. Guess email is the way to go. Webform is also OK, but that leaves no paper trail on my end, so I'd probably go for the email option.
Does your letter say you have xxx number of days to get the documents in order? Mine said "as soon as possible." To be safe, I will try to get everything turned around in 30 days.