unfortunately, this is a limitation in the way the packages are calculated, they are calculated as one package per line item.
you can get around this by setting the option in the add to cart for If Item In cart to Add New instead of sum.
this will cause the cart to add a new line item if the item is already in the cart so that the packages will be calculated properly.
As for the price difference, make sure that the service you selected in the UPS Server Behavior is the same service you are selecting when comparing online. It is most likely giving a different price online because you are not selecting the same service.