I have two ways of shipping two different types of products and I'm not sure if there is a solution using existing tools to calculate cost effectively. Hoping for some advice.

1. Standard shipping - most products are $10 flat rate per cart, but certain specialized products are $25/$45 per product.
2. Crate - $393 flat rate for any number of any type of product.

I've been able to implement the standard shipping scheme by putting the "$10 flat rate" products into a "flat rate" warehouse. This allows a customer to order just a $25/$45 "per product" product with no $10 "per cart" charge, but if they add other products they additionally incur the $10 flat rate per cart charge.

The crate scheme works, but when I add an item with specialized per product shipping cost and an item from the flat rate warehouse it adds the $393 charge twice ($786). Is there a different way that I can work out the standard shipping scheme, or a way to make the crate shipping not charged twice when the products are shipped from different warehouses?