How do I set up 2 separate shipping charges per order?

I recommend that you absorb the cost of the shipping for one of the fulfillment centers and treat it as a cost of sale. This will be far easier than setting up double-shipping.

As a merchant you want your shipping, in the long run, to break even. Work out your average shipping cost using your past orders and set your shipping prices to cover the average that you have worked out. Don't try to get every order perfect.