Power Store is a pre-built solution.
You cannot create a new cart object and tie it into Power Store, you could use eCart to modify power store though.
you can use eCart to edit the power store cart object to add discounts or charges.
the WA_eCart_Definition_PHP.php file contains generic ecart code used by any cart object, it will not need to be uploaded to the server each time.
As long as you are editing the WA_Store_Cart cart object, and not removing any of the cart columns, there should be no effect on the checkout process.