I am having trouble figuring out how assigning a new section to your folder(s) in the admininstrative piece actually changes the look of that site. How is the section name/ID/whatever tied to some sort of page layout or such?
Basically, you go the the set-up section of the admin interface create the sections and then click on assign, browse folders and select to assign to that object+subfolders/objects
As for the sections <-> layout, it is exactly as John said. In site.ini(.php) you specify which design folder is used for your site. You would create a new design folder for any custom site you make. First, ez publish looks for <yourdesign>/override/templates/pagelayout_section_N.tpl where N is the current section number. If not found it looks for <yourdesign>/templates/pagelayout.tpl for the general layout/css etc.
If that is not found, it looks for the default design specified in the site.ini(.php). That should be "./standard/...".
For more info take a look at http://ezwiki.blanko.info/index.php/Custom%20designs%20-%20directory%20structure%20explained%20%283.x%29
Karsten
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