Hi Subash,
I'm not sure I follow the issue completely, but my understanding is that when doing the import, you don't have a way to identify the campaign you are creating in MJS to the corresponding entry in your local feed.
If that's the case, you might want to switch back to CampaignService, so you could create one campaign at a time, and associate its ID to your local ID immediately when the call returns. Another option is to continue using MJS, but create the campaign initially while encoding your ID into the campaign name (e.g. [12345] Campaign Name). Once the campaign is created, you can rename it after doing the necessary local association.
AdWords API doesn't provide a way to add custom metadata to an AdWords object.
Cheers,
Anash P. Oommen,
AdWords API Advisor.