migrating muliple databases

I have 2 databases db1 and db2 in symfony2 + doctrine2 and both databases are different from each other in terms of tables and their fields.
I need to work on migration. Things work fine as long as there is one database.
But it does not works when there are more than one databases as it tries to migrate from all files [some of which are for db1, and some of them are for db2]
Also, is there any way where I can provide entity manager specific migration settings. Or is there any way through which I can provide connection or entity manager in the migration class.