You should use the Alternate Themes settings to define alternative layouts when the url matches a specific regular expression.
For example, we have a Plone site named "Plone" and accessible at url localhost:8080/Plone. To provide a different layout for the Home page, we can define the following in the registry (or TTW in the Plone Control Panel > XDV Settings section):
<record field="alternate_themes" interface="collective.xdv.interfaces.ITransformSettings" name="collective.xdv.interfaces.ITransformSettings.alternate_themes">
<field type="plone.registry.field.List">
<description>Define alternate themes and rules files depending on a given path. Should be of a form 'path theme rules' (or 'path rules' with xdv 0.4), where path may use a regular expression syntax, theme is a file path or URL to the theme template and rule is a file path to the rules file.</description>
<required>False</required>
<title>Alternate themes</title>
<value_type type="plone.registry.field.TextLine">
<title>Theme</title>
</value_type>
</field>
<value>
<element>^.*/Plone(/)?$ python://my.xdvtheme/templates/alternative/index.html python://my.xdvtheme/rules/alternative/index-rules.xml</element>
</value>
</record>
This way, the home page will use the alternative layout, while all the other pages will use the main layout specified in Theme template and Rules template
You can provide multiple definitions according to the different sections of your site.