If you change the templates using Theme-it, the changes should be applied to the rest of the pages as a template. You should look in the Templates folder and modify those using Theme-it. If saving the template doesn't automatically ask if you want to apply the changes to files, you should go to Modify->Templates->Update Pages... and make sure the first drop down says Entire site, the second dropdown is the site you're editing and Templates checkbox is checked. Then hit start and this should apply the template to the pages.