Thanks Jason - it was actually quite easy to do, so I'll explain it for others who might be interested.
First of all make sure the express checkout works properly with the original set up.
BACK UP the 'cart.php' and 'checkout.php' pages!!
Open the checkout.php page - copy the 'Authentication for PayPal Express Checkout' behaviour code and also the line:
<?php require_once("../WA_eCart/PP_ECO_Scripts/PP_ECO_PHP.php"); ?>
Copy the PayPal Express button from the checkout page, and paste it in place of your 'checkout' button in the cart form (I used a custom button).
In your Server Behaviours panel - double click the 'Authentication for PayPal Express' and change the trigger to: 'Button: PayPal_ExpressCheckout_button pressed'.
Then remove the 'ecart checkout button' behaviour as it is no longer needed.
Thats it - a far nicer solution I think.
I'll post the example page when its live!