In order to create an appointment type with different charges for additional animals, you'll want to navigate (from the "gears" menu) to "Appointment Management" --> "Appointment Types". When creating an appointment type, the first service item you select will be the "primary" service fee, and you can add an optional "secondary" service item from "QuickBooks Inventory Item for Additional Patients":
In this example I've selected "Litter Exam - additional animal" as the secondary fee. When I check-in an appointment with multiple animals, the system will apply the primary fee to the first animal's invoice, and all other invoices will be charged the secondary fee.