Currently we are upgrading/migrating FileNet from v5.1 to v5.5.8 . We already migrated some of our application which are running on v5.1 to v5.5.x successfully .

Now for our next project for upgrade/migration of another application , where we have large no. of application having larger business impact , it is not possible for us to Go-Live in a single weekend . So we are thinking to Go Live in chunks , in 2 parts . This means it Would require GCD copy to be created and moved to v5.5 along with Object Stores in tranches . Is it possible to create multiple copies og GCD in 5.1 and work on it to upgrade to 5.5 in tranches of different set of applications/object stores.

You can go-live in "chunks" but you can't split the GCD. What you do is take a copy of the 5.1 GCD bring it to the new 5.5.x environment and have it upgrade. Once that happens you should not make any changes in the 5.1 environment that would affect the GCD; for instance, don't create new object stores, fixed content devices or marking sets. As you are ready, back up the 5.1 object stores, restore the backup to the new 5.5.x environment, update the data sources in the 5.5.x environment to point to the new database, and update any file storage pointers to point to new 5.5.x locations as needed. Once the CPE finds the new object store database, it will automatically start the upgrade of that object store.

As I understood , let's say if we have 10 object store , Initially I can go upgrade from 5.1 to 5.5 with GCD & any 5 object store out of 10 object store in 1st weekend and in 2nd weekend I can go with rest 5 object store . On 2nd week, don't I need to migrate GCD DB from 5.1 to 5.5 again ?

That is correct. Make sure that if there are any applications that integrate with more than one application, that you upgrade those "related" object stores at the same time. Likewise, if you use workflow, that you upgrade the process database and any object stores that are used with the workflows at the same time.