Let's assume the following setup:

1. Site_one - Basic authentication
2. Site_two - External authentication

In order to disable external authentication on Site_one, one may have to make the configuration as close as possible to the end result i.e. configure one site with basic and another with external authentication. The site with basic authentication will still have external authentication enabled that need to be disabled in order for all sites to operate.
 

Spotfire Server 7.10 and higher

To make a manual override.

1. Make a configuration as close as possible to the end result
2. Use configuration tool to export the configuration to disk.
3. Open the configuration xml file in a text editor
4. Add the override, example:
​

    ...
    <external-auth>
      <enabled>true</enabled>
      <enabled site="nameofsite" operation="override">false</enabled>
      ...

This example has external authentication enabled an all sites except for site with name "nameofsite".

5. Import the configuration to the database again and restart all server.

This type of configuration override is possible for more settings than just the one in the example.

It's possible to configure sites with different authentication methods. One example is to have one site with basic / username and password login and another site configured for external or custom authentication. However, even if this type of setup is supported the graphical configuration tool does not let you create all possible configurations when working with multiple sites because the tool changes the configuration for both sites even when a site specific configuration needs to be made.