Hi,
those would have separate structures and therefore need their own .rsd / metadata handling. If the structures nest into each other you might be able to use the MetaDataDiscoveryURI parameter. For XML you point this at an .xsd, I assume you somehow point it at a JSON Schema but have never tried this.
If you have separate files with no common schema, you will most likely need to generate separate .rsd for each table / file. In short: using GenerateSchemaFiles > OnUse, modify them to your needs, add the names of those schemas to Schema > Tables, set GenerateSchemaFiles to Never.