The easiest way to change the layout of a Freeform report is to set up the layout in a grid then to convert it to a Freeform report.

If you want to change the layout from the Excel sheet, don't change the location of the Freeform report's top-left data cell.

In the examples below, the location of the Freeform report is C9 (top left data cell).

The example below shows a wrong layout. The original top left data cell has been changed from C9 to C10. C9 is no longer a data cell.

The example below shows the correct layout: C9 is still the top left data cell.

The example below shows an incorrect layout. The original top left data cell has been changed from C9 to D9, and C9 is no longer a data cell.

The example below also shows another incorrect layout. C9 is still a data cell, but the filter dimensions aren't aligned with the outermost row dimension.

The example below shows the correct layout.

Make certain you add any additional filter dimensions right above the existing ones. 

If no member is specified for a filter dimension, the dimension is ignored, and the data won't change.