The shipping that is provided in the PowerStore is basic shipping quote info that is returned from one of the supported carriers. If you would like to add in your own custom shipping charges you would first need to make sure that you update the files for the cart to allow for this updating. Once you have done this you can then use eCart to create the new shipping charge rules that you need.
Before you create the new charge rules you will need to know how you would like to go about charging shipping including the circumstances and amounts. Once you have decided on your shipping charge criteria you can then implement the rules that will give you these results. If you have not seen it already the eCart support page has some resources on it that could help you, specifically there is a video on discounts that would help you understand how you craft these type of rules. Shipping, discount and charge rules all use the same interface and work the same way.