Is it possible to have the customer pay the credit card fees when they complete the invoice instead of deducting it from my sales invoice?

Let me provide you a few information about credit card fees, useralexander1.

When processing payments using Merchant Services, being able to add the credit card processing fee for your customer's invoice isn't applicable. The credit card processing fee is charged every time you do a transaction. 

On the other hand, you'll want to add the processing fee to your invoices. Here's how:

1. Go to Sales then choose Products and Services.
2. Click on New then select Service.
3. Enter the name of your service item. (Example CC Fee)
4. Select the account you'd use to track our processing fees under the Income account drop-down.
5. Click Save and Close.

Once done, you can now add the fee as an additional item every time you want to charge your customers.

For reference, you can run reports in QuickBooks Online so you'll know about different aspects of your business.

@useralexander1 

It is possible but you will need another app to integrate with your QBO account.