Hello there, @info863.
You can generate a regular invoice and select the account where the amount is deposited upon receiving payments. This way, the payment will be linked to the invoice created.
To do that:
Once done, let's proceed with receiving the payment so the invoice will be marked paid. Make sure to choose the account where the money was deposited.
To give you complete details in creating invoices and receiving payments in QuickBooks Online, please see this link: Create invoices in QuickBooks Online.
I'm also adding here some great resources that you can check out about making bank deposits, and recording customers refund, in case you need it in the future:
I'll be around to lend a helping hand if there's anything else that you need, info863. Thanks for coming, and take care!