I am not quite sure if it is multiplexing you want - it sounds more like multiple streams per policy. Multiplexing aggregates several data streams from different clients/policies on the server side and writes them to the same tape. Multiple streams, on the other hand, take the backup selections specified in the policy and breaks them down to individual streams, each sent simultaneously to different drives. Multiplexing is usually only recommended if you are unable to feed a tape drive fast enough that it has to start and stop waiting for buffers from the clients - having several clients feeding the drive allows the backups to run more efficiently, but it also makes restores very slow because the multiplexed jobs have to be disentangled first. I have always found the tradeoff unfavorable, but it depends on your environment.
In your particular case, at least as far as I understand your description, multiplexing would not really have any advantages.
As the previous poster suggested, the best way to separate the last directory from the others is to create a different policy. If you were backing up a single client with several filesystems, you could use the NEW_STREAM directive in the backup selections dialog to generate multiple streams. For example, if you have the following entries in your backup selections
dir1
dir2
NEW_STREAM
dir3
the backup of this policy will create two jobs: One backing up dir1 and dir2, and the other will back up dir3, and the two jobs will run simultaneously (only if your jobs per client setting is set higher than 1, of course.) I never create policies with multiple clients, so I have no idea how you could do this in such a policy.
You could also simply try to allow the policy to create multiple data streams. Finally, you can combine this with multiplexing if you cannot feed tape drives fast enough.