Was your custom design work for the left column navigation for your categories, etc?
If the navigation was a graphic you are going to have to make another graphic for that new category. To get the link for the new category you made, go to your site html area in your admin panel to the navigation bar editor and check the dropdown bar underneath the html to load default and custom (load custom first). Then go to your store mode, click on the link for your new category and copy the link to your new graphic you made for your category in your custom navigation back into the navigation bar editor.
Hope that helps