I've been having a bit of an experiment with Sharepoint 2007 and creating a Site of 'Publishing Site' type. The best thing to do is make it a top level site and that way it's master pages are used when you create Pages and it uses the Page Layouts etc. within that Site (unless you really want to share Page Layouts across different web sites).

Changing the Page Layout
You can change the Page Layout of a created Page by going to Page | Page Settings in the Page in a web browser.

Changing the Master Page
You can change what Master Page it is using from the Sharepoint Designer by selecting the Page file and going Format | Master Page | Attach Master Page...

There are a few quick tests I like to do in any CMS.

1. Creating pages and including them in navigation drop down menus.
2. Creating a summary list of child pages e.g. a Articles list showing title, date and author