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Currently, you'll have to manually match your downloaded transactions with your invoices. I'll pass this along to our product team to let them know of your business needs.
Here's an article for more information: Match and Categorize Bank Transactions in QuickBooks Online.
On the other hand, you'll want to use bank rules to automatically categorize your bank transactions: How to Set and Use Banking Rules for Downloaded transactions. However, this automatic matching of transactions depends on the bank rule's set up.
Please get back to me if you need further assistance. I'll just be one post away if you need more help.