Increased sidebar width header code conflicts with site logo displaying

I just updated to DW Focus 1.0.7 (from 1.0.4) and am putting in all the previous customized codes, including the header and footer code prescribed in this question from last year to increase the width of my sidebar to accommodate 300px width ads. However, when I do that, the site will not recognize the site logos (large and small) that I uploaded in theme customization. When I remove the codes, the logos display fine, but then I can not display my ads in the sidebar.
Please help.