WooCommerce & Shipping

I have a problem that I feel like I'm making bigger and more difficult than is necessary. My hopes are someone here can help set me straight.

My client has two products - A and B. Shipped individually, both ship for the same amount.

The challenge starts when customers order more than one. For example:

If a customer orders 2 of product B, due to the packing (items are fragile), the box is quite large and the shipping is fairly expensive - how do we account for that when the customer is checking out? You can include dimensions for each product separately but how to you calculate shipping on combinations of products placed in a bigger box?

Flat Rate isn't an option, it is but not what we want to use if it can be avoided. We'd like to find a way to calculate shipping per order.

We're using the Fedex Basic plugin put out by wooforce. It's not doing the trick.It's calculating shipping based on weight and destination. Which is fine, until someone orders 2 items and then the size of the box causes shipping to be more than what's calculated based on weight.

I hope this makes some sense and that someone can set me on the right path - again, I feel like the answer is right in front of me, I just don't have enough experience with WooCommerce to see it.

Thanks!!