You should apply [FaultContract(YourFaultClass)] attribute to method which will throw fault exceptions.
[OperationContract]
[FaultContract(typeof(YourFaultClass))]
void Foo(int par1);
How to throw it from service:
throw new FaultException<YourFaultClass>(new YourFaultClass());
for more help have a look at: http://msdn.microsoft.com/en-us/library/cc949036.aspx