Hello there, shawncasper@gmai.
Currently, your customers can only pay the e-invoices one at a time. Hence, you'll need to send the invoices individually. If you want to receive a bulk payment for multiple invoices, you can ask your customer to pay via bank transfer or ACH.
Then, you can record the payment in QuickBooks Online manually. When paying the invoices in QBO, make sure you deposit the payment to the Undeposited Funds account. You can use this link for reference: Deposit payments into the Undeposited Funds account in QuickBooks Online.
Once you have received the actual payment, you can already create a bank deposit: Record and make bank deposits in QuickBooks Online.
Let us know if you need anything else. Have a great day!