What I have done in the past is to weigh and price both packages to the most remote zip code from me. Add them together and then plug it in as fixed price shipping.
Whether you refund shipping for buyers that buy closer to you is up to you, but I generally do if the cost exceeds 10% of what the buyer paid.
When you go to ship the item, print the first label, then go back into your orders, select "print another label" and print the 2nd label.
You shouldn't have to upload the additional tracking number manually but be ready to do so if needed.
