Akshat, I'm not following you completely. But, let me try answering. If you have partnership, NameID can be anything to be searched on; e.g. uid or email. The user should be in user store where the user got authenticated from. If you want to pick NameID value from another store, the mapping of attributes (between directories) for a user can be done using identity mapping (IDENTITY_MAP feature).
See this, for example, in R12.52:
Directory Mapping Examples - CA Single Sign-On - 12.52 SP2 - CA Technologies Documentation
Identity Mapping by Complex User Search Criterion
Or, can be done with custom code in AGP (Assertion Generator Plugin).
Customize SAML Assertion in Java - CA Single Sign-On - 12.52 SP2 - CA Technologies Documentation
Also, please see this discussion in the Community for the above:
Identity mapping for Federation
Rgds. - Vijay