I'm not sure... What documentation did you follow to implement the TotalPrice and TotalShipping calculations? I imagine it should be included in that. There are other ways it could be accounted for too. I'm just suggesting one way to account for it.
The problem is that the TotalPrice has to be the same as the sum of the individual prices or paypal will think there is a mistake and will reject the order.
The solution is to make sure the numbers add up. That means either account for it in both places or in neither place, but you can't change one without the other when using paypal.