Hello there, @Total Air.

Thank you for posting here in the Community. I can share some clarification about how the account balances work in QuickBooks.

You don't need a journal entry to clear the balances. When entering payments, please make sure to select the sub-accounts instead of the parent account.

The process will zero out the balances, including the parent. Check out these screenshots for your visual guide:

For additional reference, I've attached a link you can use about reconciling an account: Reconcile an account in QuickBooks Online.

Please let me know if you need anything else. The Community and I will be here to help you.