If you are using the FatFreeCart.com service, first please bear in mind that we provide that on a strictly do-it-yourself basis with no support whatsoever (that's a major reason it's free :^), so you're expected to troubleshoot any issues you may have with that. If you decide to upgrade to an E-junkie cart subscription (aka "FatFreeCart Pro"), that does of course include support. Since we don't officially provide support for FatFreeCart, we're not actually very well-versed in it, but that said, we will try to address your inquiry this time.
FatFreeCart only allows you to set a flat shipping rate for the first item and each-add'l-item of each product. E.g. if you Add to Cart one unit of Product A and one unit of Product B, the first-item shipping charge for each product would apply. You could set the first-item and add'l-item charges the same for all products, and then use the Handling charge to effectively "boost" the shipping amount added for the first item regardless of product, since Handling only gets added to the cart's shipping fee once per order.
If you subscribe to use the E-junkie Cart system, that uses a much more sophisticated and flexible Shipping calculator. This help page explains E-junkie's shipping calculation settings:
http://www.e-junkie.com/ej/help.shipping.htm
