1) using paypal advanced as the gateway, you need to implement SSL on your site and access the checkout using the HTTPS address
2) Where you are using options that effect the price, you need to edit the code that passes the transaction information to paypal to use the truePrice calculation intsead of passing the price.
in the webassist/ecart/PP_PayAdv_PHP.php file, change:
$vars[] = 'L_AMT' . $item_count . '=' . urlencode(number_format($cart->DisplayInfo("Price"), 2, '.', ''));
to:
$vars[] = 'L_AMT' . $item_count . '=' . urlencode(number_format($cart->DisplayInfo("truePrice"), 2, '.', ''));