Haha, the magic is called Firebug, and you can have it, too. Free. Or use equivalents in almost every other browser - just don't ask me on IE. I don't use IE, never will.
Instead of counting both produts, it adds them as a different product? Why
I don't know what you did to get this product twice into the cart, but normally, if you add it multiple times, it will still be only be one item line in the cart, only the quantity increased. It only proves you have chaos with your menus and modules leading to the same product being "technically" listed twice in your store. This also explaining the previous "problem". Clean it up, possibly start over fresh with all-new menus and modules. It's still early in the game, hardly anything in the shop.
We all got it to work, and so will you if you follow documentation etc.