Hello there, alippiatt@bioinf.

I can share the details on how you can match your transactions using the invoice number. 

Setting QuickBooks to automatically match the bank transactions using the invoice number is currently unavailable. You'll need to manually match them using the Find match option to apply the transaction to the correct invoice number.

I'm leaving you this recommended article. This will provide you with more information on how to manage your bank transactions in QuickBooks Online as well as on what are the options you can choose to allocate them: How to set and use banking rules for downloaded transactions.

If I can be of additional assistance, please let me know. I'll be more than willing to lend you a hand.