I'm not sure if I understand correctly.
But each imported / attached schema file already has it's own module and there is no way how to separate entities inside the module to regions based only on the imported schema.xml file.
Also there is no way how to import two different schema files into one module. It's necessary to have one module for each exported schema.xml file. Each module has defined its own output schema.xml file. Without that there is no way how to distinguish entity destinations.
Everytime when you attach new schema.xml to project, ORM Designer creates new module, defines import/export path to this file and imports all entities inside this module:
Could you please send more detailed description what is a required goal of your idea?