for paypal standard and sagepay updates, you will need to re run the checkout wizard.
For PayPal Payments Pro and Express Checkout updates, you can double click on the server behaviors to have the code regenerated.
the server behaviors to update are:
checkout.php -> Authorize Payments for PayPal Express Checkout
confirm .php -> Local Checkout.
after updating the behaviors, make sure to uplaod the WA_eCart folder.
because of the way that paypal payments standard works, the email conformation needs to be added manually.
payments stadard does not process the transaction in real time, you need to set up an IPN Page that will send the email when the transaction is processed. see the paypal documentation on IPN: