I created a custom page for each category that I wanted to add my style to, but I did keep most of the sub categories.
The reason was, so that I could show a different image for the link from the category page than the detailed image of the actual product. We used boxes for our product on the category, and the image of the hose on the legs on the details page, but didn't want a mix of both on the category page, for those that we didn't have a detail image for.
So I left the items that still had a subcategory linked to the subcategory pages, but the items that were linked directly from the main categories without a subcategory, I don't have linked to a category at all. There was no need to attach them since we were not using the

category anymore.
I do have a robot.txt Disallow for the old category pages, so that the search engines will stop crawling and listing them, and after a month or so the new pages were found and crawled from the links on the main page and my sitemap.xml.
Of course I also had to do a source look up of the page and pull off the left column code for the category menu. I had to take out the draw command for the categoriesandsubcategories and had to customize that menu with links to the new pages instead of the links to the

categories.