Fees can be configured to have fixed and percentage amounts at the same time. When creating a fee at Stores → Configuration → Amasty Extensions → Extra Fee → Fees → Add New Fee, go to the Options tab and click Add Option button to have as many options as you need. Name them, enter the values and choose the type.
On the storefront, a fixed fee will always have the value that you set in the backend, and a percent fee will be calculated proportionally depending on the subtotal: