How do I set up the 3% I pay when a customer uses a credit card that they pay the 3 % when the transaction is made as a service fee.

It's good to have you here in the Community, peter.  Setting up a service fee for an invoice seems essential in your business. Let me help you with this. 

You can charge a service fee to a customer for the product they're buying. In adding a charge, you may also add a message to inform your customers about the service fee. Since the invoice has already been paid, you can add the service fee by editing it. Follow the steps below to proceed. 

Creating a service fee item is the first step. Here's how:

1. In Settings, select Products & services.
2. Choose New, then click Service.
3. In the Name field, put a name for the service.
4. From the Category dropdown, select the category that best describes the fee.
5. Hit Save and close.

Once done, you can add a service fee to invoices:

1. Go to Sales, then select Invoices.​
2. Select the invoice you want to add a service fee to.
3. Select Edit Invoice.
4. From the Product or Service dropdown, select the service fee you created.
5. In the Amount field, put the amount of the service fee.
6. Add a note about the fee in the Note to Customer section.
7. If finished, click Save. 

After you have set up the service fee, it will be reflected once you print the paid invoice. 

Moreover, visit this link as your reference on receiving and recording payments in QuickBooks Online: Record invoice payments in QuickBooks Online. 

You can comment below in case you have other questions about managing invoices. I'm always ready to help you. Have a good one.