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The logo centering should work using text-align:center, I tried it using firebug and it seemed OK. Try wrapping the code for the logo inside a dive with the align set to center
<div align="center"><img height="50" align="center" alt="" src="http://i.nixle.com/uploads/support/images/badge2.gif" />div>
As for the columns issue look at your themes css file and see if the right column is set to a specific width such as width:150px;
If it is set to a width smaller that your element (like the homeland security thing) then the column will expand to fit the width of the element.
See if your columns is a set width, you can edit the width of the advisory image to be smaller.
<img width="177" height="20" border="0" src="http://www.nationalterroralert.com/advisory7.gif">
change the value of width="177" to the same widht as the right column and change the height="20" value to keep the same aspect ration, the only thing is the image might not look great if the size is reduced.
If you are wanting to have both columns the same width you would have to modify the theme to make right and left columns wider and set them to be the same width in the css, but if you insert wider images, etc it will always make the columns wider.