Use the MDT Vault, you have the option of selecting what part or subassy to copy for the new assembly. My favorite opion is to put all parts into one folder, and then copy and paste mannually using Windows Explorer.
Thank you for your help and I feel odd asking such a simple question.
Step:
1) Open vault for the first time.
2) RMC Add file Battery box assy.iam
3) Press OK, Then some box with Relationships and Inventor add-in I pressed YES.
4) RMC Copy Design
ERROR File Cannot Be copied
Could not locate associated project file in vault