Here's the easiest way to make sure this works:

1. Duplicate preload.fla and name it something else (like customPreloader.fla).  Make sure you go into your publish settings and change its publish path name to match the new name.

2. Open the new fla file and set the tint on the preloader clip on the stage to red or something.

3. Publish the swf.

4. Open your site.xml and add the indexFirst="true" attribute to the site node.

5. Add an asset to the index page:

Code:
<asset id="customPreloader" src="customPreloader.swf"/>

Then, inside your index page transitionIn() method:

Code:
Gaia.api.setPreloader(assets.customPreloader);

You should see the normal site preloader for the index page and then see the red preloader for the rest of the site.

This is always a good starting point.  You can then duplicate the Preloader.as and PreloaderScaffold.as files to customize the custom preloader.