Chris,
> how to configure this feature using a separate VCS root
Should be quite straightforward to create a new VCS root pointing to a separate repository which is going to hpld the settings and select the root int he Versioned settings section of the project.
You are welcome to ask specific questions in the <a href="https://teamcity-support.jetbrains.com/hc/en-us/community/topics/200366709-TeamCity-General-Topics" rel="nofollow">forum</a>
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