Building up on Sjoerd solution to add alignment to a manipulate object :
Consider the following :
Manipulate[
Panel[Style[Row1, Bold, 20],
ImageSize -> 150, Alignment -> Center]
Panel[Style[Row2, Bold, 20],
ImageSize -> 150, Alignment -> Center],
{{Row1, {1}}, {1, 2, 3, 4, 5}, ControlType -> SetterBar,ControlPlacement -> Left},
{{Row2, {2}}, {1, 2, 3, 4, 5}, ControlType -> SetterBar,ControlPlacement -> Left}]

Is there a way to have the panel on top of each other aligned with the corresponding SetterBar ?
Would something like this work?
This technically moves the controls into the body of the manipulate, and prevents the actual controls from showing up where they normally would.