To edit shipping, you would have to open the eCart object and go to the shipping tab to change the shipping rules.
Using Paypal Payments Pro or Authorize.net will allow you to have credit card payments, it is just processed through a payment gateway.
To change the payment gateway, you would want to remove the checkout pages (checkout, confirm, success, failure, pp_confirm, pp_success, pp_failure) and apply the eCart wizard to the cart page.
Changing these and having it work with PowerStore will require some custom coding, which is not supported, so you would have to implement the changes on your own after what I've instructed.
By using the eCart object that is already generated for PowerStore to generate the pages, the PowerStore and eCart checkout pages will be linked.