<?xml version="1.0" encoding="UTF-8"?>
<mm:MyMM xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:mm="http://myMetamodel/1.0">
	<!-- Somes entities from my metamodel -->
	<object name="object 1">
		<associations links="//@object.2"/>
	</object>
	<object name="object 2" />
	<object name="object 3" />
</mm:MyMM>

<?xml version="1.0" encoding="UTF-8"?>
<mm:MyMM xmi:version="2.0" xmlns:xmi="http://www.omg.org/XMI" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:mm="http://myMetamodel/1.0">
	<!-- Something like this -->	
	<import href="platform:/resource/model1.model" />
	<object name="object 4">
		<!-- Link object 4 to "object 2" from "model 1" -->
		<associations links="//@object.2"/>
	</object>
</mm:MyMM>

public static void main(String[] args) {	
		ResourceSet rs = new ResourceSetImpl();
		rs.getResourceFactoryRegistry().getExtensionToFactoryMap().put(Resource.Factory.Registry.DEFAULT_EXTENSION, new XMLResourceFactoryImpl());
		
		URI uri1 = URI.createPlatformResourceURI("/project/subModel1.model", true);
		Resource resource1 = rs.createResource(uri1);
		SubModel1 root1 = MyMetamodelFactory.eINSTANCE.createSubModel1();

		resource1.getContents().add(root1);
		try {
			resource1.save(System.out, null);
		} catch (IOException e) {
			e.printStackTrace();
		}
		System.out.println();
		
		URI uri2 = URI.createPlatformResourceURI("/project/subModel2.model", true);
		Resource resource2 = rs.createResource(uri2);
		SubModel2 root2 = MyMetamodelFactory.eINSTANCE.createSubModel2();

		resource2.getContents().add(root2);
		try {
			resource2.save(System.out, null);
		} catch (IOException e) {
			e.printStackTrace();
		}
		System.out.println();
		
		URI uri3 = URI.createPlatformResourceURI("/project/model.model", true);
		Resource resource3 = rs.createResource(uri3);
		Model root3 = MyMetamodelFactory.eINSTANCE.createModel();

		root3.setSubModel1(root1);
		root3.setSubModel2(root2);
		
		/* I also tried this :
		root3.setSubModel1((SubModel1)resource1.getContents().get(0));
		root3.setSubModel2((SubModel2)resource2.getContents().get(0));
		// */

		resource3.getContents().add(root3);
		try {
			resource3.save(System.out, null);
		} catch (IOException e) {
			e.printStackTrace();
		}
}

<?xml version="1.0" encoding="ASCII"?>
<mm:SubModel1 xmlns:mm="http://myMetamodel/1.0"/>

<?xml version="1.0" encoding="ASCII"?>
<mm:SubModel2 xmlns:mm="http://myMetamodel/1.0"/>

<?xml version="1.0" encoding="ASCII"?>
<mm:Model xmlns:mm="http://myMetamodel/1.0">
  <requirementModel/>
  <analysisModel/>
</mm:Model>