You can add role on your configuration into your patch config.
For example I created a patch config for setting up site definition for prod environment.
If you need Unicorn to publish to two different databases then yes, adding it to the list of TargetDatabases is the way to go.
As with anything Sitecore, I would not recommend modifying the configuration file directly, rather to patch the value in.
Also be mindful that a few compatibility issues snuck in on recent Sitecore releases, so you should aim to get ...
I fixed it.
I was referring to Helix's Unicorn project.
It seems that the problem was the following. In Foundation.Serialization.Base.config
<dataProviderConfiguration set:enableTransparentSync="$(env:UNICORN_ENABLE_TRANSPARENT_SYNC)" />
I deleted here.