I am not sure about the first half of your question—the KPI bit, @Muna Shabab. In a report table component, you can definitely have different filters on different columns.
Maybe if you would detail a bit more what you mean with "different areas that are isolated by the different filters", I could help some more.
By looking at the KPI component in Reporting Studio in CT, I would say it can't be done. You seem to be able to compare different metrics, but not the same one:
I put together Cost and Cost YTD to build a KPI with two metrics, but the filter applies to both, so it's not what you want. Short of having two KPI components, one for each of the groups you're after, I don't know how I would do what you write.
Not sure about Apptio BI, haven't done that much with it in recent times.