Hi Mad.
The cargo config is just a representation of what can be loaded. This then writes to the aircraft.cfg file and the aircraft flight model behaves as though it is carrying the weight and the distribution of the cargo.
The fuel low warning is another problem that some people seem to have and the CS team have given a solution here

http://www.captainsim.net/yabb2/YaBB.pl?num=1145014612

Hope this helps.

Dax