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.