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You can accept your customer's payments with multiple payment methods in QuickBooks Online. However, you have to apply it one at a time.
Here's how:
- Go to the + New menu and then select Receive payments.
- Choose the name of your customer.
- On the Payment method column, select Check.
- Select the correct account from the Deposit to drop-down menu.
- In the Amount received field, enter the payment received.
- Choose the invoice you're recording the payment for.
- Once done, click on Save and close.

- Repeat the process when applying for the credit card payment.
For more details, please see this article: Record Invoice Payments in QuickBooks Online.
Additionally, I've added an article that'll help you deposit the payments in QuickBooks Online. This ensures the program matches your real-life bank record: Add the Funds to the Correct Accounts.
If you have any other questions in mind, you can leave them below. I'll get back to you as soon as I can. Have a great rest of the day.