Welcome to the Community, Amupton.
Thanks for reaching out here for support. Let me provide information about your concern.
When you Make Deposits in QuickBooks Desktop, there's no need for you to select an account since your payments will be listed on the Payments to Deposit window. You'll just have to select those payments.
Please check this out:
To learn more information about recording and making deposits in QBDT, please check this article: Record and make Bank Deposits in QuickBooks Desktop.
I'm also adding this article on how to handle bank deposits for your reference.
You can always go back into this thread if there's anything else you need.