Hello there, Cpattison1.
The QuickBooks Payments settings might have been set up to only download the payments in one account. You can reach out to our Merchant Support Team to check the information and walk you through with the changes.
Here's a link to get our contact information: QuickBooks Payments Support
In the meantime, you can assign the payments from the QuickBooks Payments page to the Undeposited Funds account. Then, manually deposit them in QBO. Please see this article for the steps: How to record bank deposits.
Should you have other questions or concerns, feel free to visit us again. Thanks.