I'm not sure this is what you mean, but I was looking for a way to customize the order in my stacked column chart. It seems that the order is fixed as the order of creation of the records. So I created an unrelated table for chart data which is only related to fusionchartconfiguration table. I made a loop script that would copy the sorted data from the original data table and then create new records in the chart data table and paste the copied data one field at a time.
It works quite well. I'm not sure this is what you meant but I see others have asked about the sorting issue in other posts.
