It sounds like you don't want the additional charge to appear in the subtotal. I wouldn't try to tweak the subtotal if you can help it. The subtotal would just include the additional charge. You can do things like uncheck apply discounts, make it free shipping, and make it non-taxable so it doesn't affect those calculations.
Here is the old thread about $extras:
http://forum.x-cart.com/showthread.php?p=185108#post185108