They are two separate backups. Time Machine will back up to whichever drive is currently connected.
I make use of this to alternate two Macs in my household between two Time Machine disks. Each drive contains a complete copy of each Mac as of the last time it was connected, as well as all past snapshots made to that drive that haven't been deleted to make space. Either one is thus useful on its own for restore purposes, even if the other is destroyed or corrupt.
If you connect two drives simultaneously, the same result occurs (each drive is a complete backup); Time Machine will alternate backing up to each.