I don't believe you can place relative paths in the root web.config, but that isn't a concern. You can use the support of nested Web.Config files to your advantage.
You can place a web.config file similar to this in any of your sub directories (adjusting to suit the needs of that specific directory) and you'll get the support you seek. It is also a lot easier to maintain as the settings are closer to the code files they control.
<?xml version="1.0"?>
<configuration>
<system.web>
<authorization>
<deny users="*"/>
</authorization>
</system.web>
</configuration>
The overall configuration for authentication types, roles, etc. would be done in the web.config in your applications root directory. As a result, you can't set a separate login page per directory from this method, but you could have a login page that automatically handled a redirect when needed (by analyzing the ReturnURL QueryString value).
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