Project billing fee

My  client has er Project Billing Busienss requirement which I think is a major gap.

Here is the Project Billing requirement They use the Fee Schedule to apply those fees per services; but some customer contains a discount % of the fees per items.
Example
Customer # 2
Weather package fees 10% discount
Over flight permit fees 2 % discount

Customer # 3
 Weather package fees 5% discount

We need to clarify how we will accommodate this request; because this is a most item.
Are we going to use our existing FEE Maintenance Workbench?
Are we going to convert their existing FEE schedule exemption by customer – items - % discount?