Thank you for visiting us today here in the Community. I can help you get rid of the error message you're getting.
You don't have to manually apply the payments to emailed invoices if your customer paid online. To fix the "A payment you are trying to download can not be matched or recorded. Please record your merchant payments manually" error:
For detailed instruction, you can refer to this article: Error in Merchant Deposits.
Let me know the results, Chris52. I'm still here to help you further if you have follow-up questions. Wishing you all the best!