Thanks for getting back to us, yodankful,

Allow me to step in and share some information with you about the employee's card balance in QuickBooks.

Making payments on the main account won't impact the sub-accounts. Thus, the balance of the sub-accounts remains in QuickBooks. The recommended solution is create a journal entry to transfer the balance to the parent account. 

I've received a similar post about fixing the sub-account balances. Please refer to this link for your guidance: https://quickbooks.intuit.com/learn-support/en-us/reports-and-accounting/how-can-i-fix-my-credit-car.... 

I've also added this article: About bank or credit card subaccount setup to help organize your Chart of Accounts in QuickBooks Online.

Should you need anything else, don't hesitate to leave a comment below. I'm always around to help you out.