Using directives are aggregated from across all the files provided, so it would be perfectly fine to define a config.scala top level and config.scala in main and test directories. However, since tests inherits config from main (so no need to define a Scala version in both) I would suggest having conf.scala and conf.test.scala top level with all configuration.
Using directives has a dedicated guide and hopefully, it will explain a bit more. In case of any further questions, we have both Discord channel and Github discussions to explain, help or discuss changes and suggestions.