Hi Janette….for transparency, this would be applied to the .sidebar container. However, you are aware that there is an opacity level setting under the Background Overlay Opacity tab in the customizer? Although this is for the image.
For the margins question, this will actually be padding for the #main container. So for example, the default padding for this theme is:
Regarding a scrollable sidebar column, I haven’t tried this, but you would do it this way:
For info about overflow: [url=http://www.w3schools.com/cssref/pr_pos_overflow.asp]OverFlow[/url]