You should start with a minimal homepage . This will be the main page associated with publication layouts. Then you can add in all the html / css you want to your main page and layouts so that they look as if you want.
If users viewing the same publication pages also need access to your list formats (new, edit, display), you will have to edit these files and attach them to your main page (either through SP Designer or in a function, it will automatically) . Or, configure the main page of the application in much the same way as the main page of the publication, and deploy them as a function using an HTTP handler that changes the main page for application.master at run time.
Also FYI, there are many problems as soon as you start customizing the list form pages for a site accessible by anonymous users, so do your research first if necessary.
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