Is there a best practice way to use a single credit card across multiple company entities and accurately separate charges and payments amongst them?

I appreciate you for reaching out to us, @user19804.

You can separate charges and payments if you're referring to using one credit card account for multiple QuickBooks Online (QBO) companies. To link a bank or credit card account in QBO, follow these steps:

1. Go to Banking. 
2. Select Connect account if this is the first bank account you’ve set up. 
3. Or select Link account if you already created one.
4. Enter the name for your credit card in the search field.
5. Select Continue. 

You can check this article for more detailed steps: Connect bank and credit card accounts to QuickBooks Online.

If you've been using a QuickBooks Payments, you can link it to your other QuickBooks Online accounts with these steps:

• Under Company Settings, select Payments.
• Click Connect.
• Follow the prompts to connect your existing account.

Please take note that you can't utilize your QuickBooks Payments account with both QB Desktop and QB Online at the same time.

This article contains detailed instructions on how to keep track of your expenses and record payments: Enter and manage bills and bill payments in QuickBooks Online.

Keep me posted if you have further concerns with your credit card accounts. I'm here to help. Have a nice day!