How can I charge the payment fees to the customers if they're paying by credit card or ACH using QBO

There is no option like that.  You have to manually add it to the invoice. 

Hi there, April. If you have a QuickBooks Payments (QB Payments) account, you can send an Invoice with an ACH bank payment.

Here are the guide steps on how to send:

1. Navigate to All apps, select Customer Hub, and then click Overview.
2. Click on Create an Invoice, then select the Manage icon.
3. Go to Payment options. Make sure all payment methods (Credit Card, ACH, PayPal, and Venmo) are disabled, and confirm that the option for Customers to pay the fee is enabled. Important: Enabling any individual payment method will result in you being charged the convenience fee instead of the customer.
4. If you have a preferred payment method, specify it in the Payment instructions or the email message.
5. Finalize the invoice details, then select Review and send, followed by Send invoice.

If you don't have a QB Payment account, create a service item for the fees and manually add it to your invoice.

To add a processing fee, click the Gear icon, select Products and Services, click New to choose Service, then enter "Processing Fee," assign the appropriate tracking account, and select Save and Close.

Once completed, add the processing fee as an additional item to your invoice to charge your customers.

Let us know if you have further questions. We're here to help you anytime.

@_AprilA 

If you need to accept B2B payments, use a 3rd party processor with the feature and sync it with QBO.