Add fee to total order balance once
This is a bit tricky, since the order total is calculated from the line items. Either you would need to add/remove a line item that has the fee, or you would need to add the price to the order after it has been loaded, using hook_commerce_order_load.

I would prefer the line item solution, as it is more robust, but it also requires more work, as you will need to define the line item and either create custom code for adding/removing it.