If you'll create separate entity manager for this second connection/bundle you will get another directory in your DoctrineMigrations dir. For example:
app/
DoctrineMigrations/
entityManager1/
entityManager2/
If you want put all migrations to another directory, you can set it inside your config.yml:
doctrine_migrations:
dir_name: '%kernel.root_dir%/../Acme/CommonBundle/DoctrineMigrations'
namespace: 'Acme\CommonBundle\DoctrineMigrations'
If you want some more complex thing like put migrations from em1 to dir1 inside bundle1 and put migrations from em2 to dir2 inside bundle2 you will need an additional two configuration files where you'll specify dirs for particular bundles:
http://docs.doctrine-project.org/projects/doctrine-migrations/en/latest/reference/introduction.html#configuration
And then you run your migrations like this:
doctrine:migrations:status --em=em1 --configuration=./path/to/bundle1/Resources/config/migrations.yml
doctrine:migrations:status --em=em2 --configuration=./path/to/bundle2/Resources/config/migrations.yml
By https://github.com/doctrine/DoctrineMigrationsBundle/pull/46
the migrations.yml file should look like:
name: Doctrine Postgres Migrations
migrations_namespace: Application\Migrations
table_name: migration_versions
migrations_directory: PostgreSqlMigrations