Adding transaction fees to orders

For our 2016 season management have decided they wish to add a transaction fee per booking with a few exceptions which we can manage using order, performance, price type, package and MOS

They would like to investigate exempting any bookings of $35 or less from this charge.

We could manage it manually over phone and at counter but that leaves room for operator error and does not solve the issue of online sales.

 Has anyone done something similar to this?