How to set up Time Machine backup for two macOS disks with third data disk? I'm hoping someone has had experience with this and can offer some advice, here's the lowdown on my scenario.

I have a Mac Pro tower (so 4 drive bays) with all bays filled.


Bay 1 has a 320GB HDD hosting Mavericks
Bay 2 has a 1.5TB HDD JHFS+ formattedd for a data/archive disk
Bay 3 has a 320GB HDD hosting Windows 7 
Bay 4 has a 120GB SSD that I just installed macOS Sierra on.


I have a 2TB external HDD that I use for Time Machine backups, and in the past I backed up disks 1 and 2, leaving the Windows disk alone, of course. Now that I have an SSD running Sierra, my goal is to use Sierra as my primary OS, and only use Mavericks when necessary. (And it is necessary, occasionally.)

Ultimately my concern is this: I do not need Time Machine trying to back up three disks to my backup disk from one OS, only to have it attempt to do the whole thing over again when I boot into the other OS. Is Time Machine intelligent enough to know that I am backing up the same three disks from two OS's?

Update: I ran Time Machine from the Sierra disk and it didn't try to duplicate the backup of the storage disk, so that's half of my question answered at least, but I'm still not sure I want to boot into Mavericks with the Time Machine disk connected until I know what to expect from it.
Time Machine backups are organized by machine directory, then by snapshot (date&amp;time), and only then by backup source (see the section on "backup structure" in the man page for tmutil). I might be wrong, but I would expect your Sierra and Mavericks installations to be considered separate "machines", even though they are running on the same physical machine. I'm not sure whether Time Machine is smart enough to realize that the backup sources for these two "machines" are the same, and to use hard links between them to avoid each machine directory to include completely separate copies.

I think the simplest thing to do would be to set Time Machine on Sierra to backup all volumes except the SSD with Mavericks, while setting Time Machine on Mavericks to only backup the Mavericks volume. Or some variation on this of course, like backing up everything using Sierra and turning Time Machine on Mavericks off.