That is exactly right Pink. And yes, it does take some work, but wow, when you finally get it all set up it is fabulous especially for those heavy items.
I've had to go back and tweak occasionally. I had an order for 10 sets of mini cupcakes and they got put in a medium flat rate box. They did fit, but I would prefer that only 8 sets go in because they are a little delicate. So I went back and added an inch to the height, and now the calculator only puts 8 sets in like I want.
And if you are measuring with bubblewrap, as you know, you can squish it a bit. So there is some give for what dimensions you put in. I originally had my pens with a height of 2 inches - but actually if I squish down on the bubble wrap a bit I can fit them into a small flat rate priority box which has a height of 1.6. So I changed my dimensions height to 1.5. Now if someone wants priority shipping, they will get the small flat rate box for up to 3 pens just like what I can fit in that box. For four or more it will either go to a Box A or straight Priority depending on their zip code and which is cheaper.