you would need to use eCart to remove the existing shipping rules and create a new one.
make sure the power store files are at the root of the dreamweaver site. Open the cart.php page and double the eCart Object server behavior in the server behaviors list to edit it.
On the shipping tab, remove the existing shipping rules. then add a new one. Set the trigger to Number of Unique Items in cart Greater than 0.
For the calculation, use Based on multiple of column subtotal:
Subtotal of Column "Quantity" Times "3" "plus" "0"
change the three to the amount per item you would like to charge.