The files are stored here on the web server: Local Drive:\Program Files\Common Files\Microsoft Shared\web server extensions\60\TEMPLATE\1033
Site customization of your site definitions (which is what you are referring to) is a broad topic. I have a lot of resources about customization here:
heathersolomon.com/blog/articles/sp2003.aspx
High level: Each type of sub area (News, Home, Topics, etc) uses a different site definition (footprint of what the area looks like and the files that are used to render the page). So you will need to either streamline and just use a handful of site definitions in your portal, or edit every definition that is in use, etc. Bottom line, you will need to repeat your edits that you have made to default.aspx to the default.aspx for each site definition you need to modify.