When installing NetBackup 6.0 or higher, you specify the name of the EMM server, which by default is the master server. The EMM database will usually reside on the master server.
The media servers don't contain any databases, or catalogs. They just control the storage unit assigned to it.
I would do "A" if the master server is at 5.x. If upgrading from 6.0 to 6.5, then no need to run the nbpushdata command. But, please refer to the upgrade guide as your #1 reference.
Upgrade the master server first to 6.5. Update the master server and all features on the master server to 6.5.4 and then upgrade the media servers and clients to 6.5.4.