With the new X-Cart 5 version you will be able to add shipping mark ups.
Also, there is a module that allows you to add payment method surcharges and discounts.
But I believe you need an unconditional surcharge depending on the order total, and this is something that you have to program as a custom module. Here is an tutorial on creating a similar module (for a discount, not for a surcharge):
http://kb.x-cart.com/display/XDD/Creating+global+discount