How to query models from different designers
When a Template is configured to be a File per Model a Designer and Model Type need to be specified under Template Settings. For additional Designers along with their Model Types to be available for selection, their corresponding Module needs installed with the Install Metadata only option checked.
For the purposes of demonstration, this how-to will explain using the Domain Designer and the Class Model Type from it.
Install the module
Install the Intent.Modelers.Domain with the Install Metadata only option checked, the option can be made visible by clicking on the Options arrow:

Select the Designer and Model Type
Create or select a Template and in the properties panel and for Designer select Domain and for Model Type select Class:

Run the Software Factory
Run the Software Factory and open the Template's corresponding Registration class.
It has generated a GetModels method that will look in the Domain for Class models using the GetClassModels() query method. When the module is run in an Application an instance of the Template will be instantiated for each Class which was modelled in the Domain Designer.
public override IEnumerable<ClassModel> GetModels(IApplication application)
{
    return _metadataManager.Domain(application).GetClassModels();
}
Other designers
For any other Designer the query will be different depending on the Designer and the Elements that's provided by the Designer, for example using the Services Designer and selecting Service as the Model Type will generate the following:
public override IEnumerable<ServiceModel> GetModels(IApplication application)
{
    return _metadataManager.Services(application).GetServiceModels();
}