If you require just a single package in the merge, just DND the EClasses etc in the Sample Ecore Editor.
If you want a multi-package merged Ecore file, you hit a limitation of the Sample Ecore Editor, so I would edit the XMI to change from ecore:EPackage root element to , xmi:XMI with two EPackages, then DD for the residue.
Not being able to transform elements of the second model seems very unlikely. Seems like you have created a new problem to solve rather than solve your real challenge. Perhaps someone on the Epsilon newsgroup can help if you explain your actual problem.
DND is easy. Create a scratch Ecore file, open with the Sample Ecore Editor and try a few drags and drops.
Thank you very much....
I use ATL as transformation language. You are right. It seems my real challenge is another thing!
Because when I register my meta-models, it doesn't generate any output whether I transform ETL part or EOL part. It has "Error loading platform:/resource/Project/Model/Tree2Graph.etl.model: org.eclipse.emf.ecore.xmi.IllegalValueException: Value 'org.eclipse.emf.ecore.impl.DynamicEObjectImpl@7eb81341 (eClass: org.eclipse.emf.ecore.impl.EClassImpl@116d8da8 (name: NameExpression) (instanceClassName: null) (abstract: false, interface: false))' is not legal. (platform:/resource/Project/Model/Tree2Graph.etl.model, 35, 104)