Product Pricing Advice

My company sells custom products directly from a manufacturer, and the manufacturer has attached fees with special rules (the fee is a flat rate that is based on the quantity of the order and all of the custom options chosen) to some of their products. Traditionally we would pass these fees directly to the customer, but now that we are pushing more into e-commerce it's getting difficult to manage and explain the special conditions and the fees.

What I'm wondering is if anyone else has similar situations with their product costs and how you have dealt with it.