Customer has paid the difference between my invoice and their invoice. How do I record this?

I can help you with recording the transaction, @DaisyParker.

You can record this as a barter transaction. You'll create an invoice for the machine you sell and a bill to record the part exchange. 

First, you'll need a barter account from your Chart of Accounts:

1. Go to the Gear icon (⚙) and find the Chart of accounts.
2. Click on New to create a new account.
3. Under the Account Type dropdown, choose Bank.
4. For the Detail Type, dropdown, select Cash on hand.
5. Set an account name and click on Save and Close.

I can see that you've already created an invoice, here's how to receive payment for the invoice:

1. Go to the + New and select Receive payment.
2. From the Customer dropdown, select your supplier’s name.
3. Provide all the necessary information. 
4. Select the barter bank account in the Deposit to dropdown.
5. Select Save and close.

Once done, enter and pay the bill or your invoice you've received from the customer.

To create a bill: 

1. Go to the + New button and select Bill.
2. From the Supplier dropdown, select your barter partner.
3. Enter all the necessary information.
4. Click Save once you're done.

To pay the bill:

1. Go to the + New button and locate Pay bills.
2. From the Payment account dropdown, choose your barter bank account.
3. Select the bill you’ve created earlier and Make payment under Balance Due.
4. Enter the amount.
5. Click on Save and close.

Check out this article for more information about entering an invoice and a bill to record the products or services you’re exchanging: Record a barter transaction.

From here, you can generate customer and vendor reports to see transactions to get insights into how your business is doing: Common custom reports in QuickBooks Online.

Let me know in the Reply section below if you have further questions about recording your transactions. I'm always here to help.