Since SQL Developer allows users to create multiple migration repositories for supporting migrations from many databases to Oracle concurrently, users have to pick the desired migration repository connection which will be used for their migration exercise.
SQL Developer also allows users to specify a particular migration repository connection as a default connection, so the selection becomes easier, particularly if there are several of them.
Note
It is better to create multiple repositories, if there are several databases to migrate (from different vendors or from the same vendor such as Sybase). This allows the migration effort to be divided into multiple groups, so that they can carry on their tasks without interfering with each other. It may also provide a security layer as to who can access the source schema/business logic.