If you are on the professional plan you create shipping templates and each SKU has a specific template assigned. You may have several different templates. If you do not specify a template when you create a listing, then your default template is used. You may change or edit templates at any time. Just remember that any edit you make to a template will affect all SKUs using it.

If you are on the individual plan you have no control. Whatever Amazon decides the shipping charge is for that item / category -- that's what you will be charging / receiving. Your only control is through adjust price of the item.