Branding for _layout Pages in SharePoint

I got a comment on one of my earlier posts about SharePoint branding (the look and feel of sites, including colors, fonts, page layouts, etc.).  I couldn’t respond directly due to the person’s communication settings on their Live Space, so I thought I’d answer it here:

Marc,
Great blog, but I was wondering if you could fill in some gaps for me.  I move elements around in my custom master page and I want those changes applied to the application pages as well.  I have been trying to find out how to do that.  I didn’t rename or remove any pieces.  I only rearranged them or made them not visible on the page.  So how can I make those changes appear on the /_layouts pages?  Thanks for any help you can provide.

Pages in the _layouts directory are actually stored in the hive on the server’s hard disk rather than in the database.  Each page is available to all sites.  These pages also have a different master page (also stored in the hive) called application.master.  Therefore, when you make changes to default.master (Don’t change it directly — make a copy — you never know when you might need to go back!), those changes aren’t applied to the _layouts pages.

What you should do is to turn your CSS into a theme and apply that to your site.  This works because the theme is applied to all of the pages, including the _layouts pages.  Keep in mind that there are some CSS classes in application.master that don’t occur in default.master as well as some different constructs, so you may need to go back and forth a bit.