Line items apply in a linear order, so it's important to ensure that they're listed in the correct order.
For example, a booking might include a flat fee and a tax. If the flat fee is listed above the tax, the tax will be applied to the booking's subtotal and the fee. If the tax is listed above the flat fee, on the other hand, the tax will only apply to the booking's subtotal.
To reorganize line items, click them and drag them up or down in the list of line items.
When they're in the correct order, click Save Changes.