I've been trying to line up my right sidebar with my center column, but playing with margins and padding in "RIGHT sidebar style" doesn't change the position of the sidebar at all.

Am I looking in the wrong area?

Atahualpa Theme Options -> Sidebars -> Left sidebar style: (and the same for the Right)
padding: 130px 10px 10px 10px;
the first item is the top padding.

Padding will push the first item in the column down that far IN THE COLUMN. The columns (left, center and right) are all aligned under the header area AT THE SAME POINT. What can happen is you can have the illusion of the sidebars being at a different height depending on the background colors of the areas.

Try this:
set your right and left sidebar background colors to
LEFT sidebar style
border-right: solid 1px #dd0d1c;
padding: 10px 10px 10px 10px;
background: #ff5800;

RIGHT sidebar style
border-left: solid 1px #dd0d1c;
padding: 10px 10px 10px 10px;
background: #b634bb;

then go to the CENTER and set
Center column style
padding: 10px 10px;
background: #00ad83;

This will set a horrible color combination, but they should be different from your layour background and then you can see where the tops of each column is. And you will see they align nicely, the problem is most likely, the padding within the column or the fact that your side bar backgrond color is one thing while the center column is the same color as the layout background.

Hope this helps

p.s. don't forget to give Flynn a donation - that's the best way to get support from him.