If you rerun the wizard you will recreate the pages for the site. However, since it is a template based site you can just update the template with the new include reference after editing the site.
For the css you can always make use of the mystyles.css file. This css file is always loaded last so whatever you have here will overwrite anything that precedes it. Also, when you have css in this file it will not be overwritten when you edit the site or run the wizard again.