We have some new shipping config features in development that are due to go live soon which may work for you, but until then, you may find it helpful to know the basic formula we follow when calculating shipping charges presently:
((cost per oz.) X (total product wt. + container wt.)) + (container cost) + (handling cost)
The (cost per oz.) part would be determined either by a flat per-oz. rate you specify for Domestic or International shipping, or otherwise by standard USPS rates if you have your zipcode entered without any custom rates in Seller Admin > Cart Shipping Settings (we compare USPS First Class vs. Priority and apply whichever rate is cheaper). Note that you can "game" the formula by applying non-literal figures for various settings, so the formula adds up the way you want. Creative examples are given on our Shipping help page:
The closest I can figure to what you describe might go something like this:
In Admin > Cart Shipping settings, delete your zipcode, set your handling charge to 3.50, Domestic rate to 1.00, Int'l rate to 1.25, leave all container costs/wts. at 0.00, and set the shipping weight in each product's configs as 1.00. This would charge 4.50 (=3.50+1.00) first-item and 1.00 each-add'l for Domestic, and 4.75 (=3.50+1.25) first-item and 1.25 each-add'l for International. You can adjust the various figures to get them to add up differently, but I couldn't quite figure how to get exactly what you'd described.