Vaults back up only Libraries. Libraries do not contain Referenced Masters. Vaults do not back up Referenced Masters.
TM is one way to make back-ups (of any files). Vaults are another, restricted to Library files (which have the extension "aplibrary"). How these back-up tools fit into your overall data security scheme depends on too many variables to give even a rule of thumb.
I try to keep three copies of all data at all time, and never have all three in the same location. A reasonalbe way to do this is to shoot to a card, copy the card to your computer and leave the files on the card, then import into Aperture and leave the files on your computer. Then after you make a backup, you can re-format your card. And after you make a second back-up, you can delete the copy of the card files on your drive. At that point you should have one copy in Aperture, and two back-ups.
This gets complex with Referenced Masters, but remains -- if I can put it this way -- straightforward.
I use TM as my first and most frequently updated back-up of both my personal Library and my personal Masters. I used to use Vaults as a less-frequently updated second back-up of my Library, and stored it off-site along with a copy of all my Referenced Masters. I now do that just with Finder (my Vaults started to have problems when my Library grew to over 100 GB).
I manage some other Libraries which I back up regularly (and the Masters, separately) to external drives. I rotate these, and never have all back-ups at the same location. I do not use TM on these Libraries.
Note that Masters need only be backed up once (but to multiple backup locations) and that backup should happen immediately after copying to the hard drive from the camera card, before involving Aperture or any other images management app.
Backup of Masters does not get complex with Referenced Masters, it is very simple because it is already done before ever entering Aperture. Vaults of course are used to back up the Library.
Time Machine is an ongoing regular-routine backup process. Image originals instead need irregularly timed backup, once.
IMO referenced Masters make far more sense than building huge managed-Masters Libraries.
• Hard disk speed. Drives slow as they fill so making a drive more full (which managed Masters always does) will slow down drive operation.
• Database size. Larger databases are by definition more prone to "issues" than smaller databases are.
• Vaults. Larger Library means larger Vaults, and Vaults are an incremental repetitive backup process, so again larger Vaults are by definition more prone to "issues" than smaller Vaults are. One-time backup of Referenced Masters (each file small, unlike a huge managed-Masters DB) is neither incremental nor ongoing; which is by definition a more stable process.
Managed-Masters Libraries can work, but they cannot avoid the basic database physics.
I really want to understand this. When you say, copy card to computer, are you copying files to desktop or to a folder with a name? IF so what do you name that folder? When you then go on to say, import into Aperture, are you importing the files that you kep on the card? Or the files that you just copied to the computer?
I think you are saying, let me see if I have this right, that the files you transferred from your card to the computer simply stay on the computer, although I don't know where you put them and name them. THen you import the files you want to keep from the card into Aperture. Now you have set of files "on the computer" (still don't know where) and a set of files in Aperture.The next sentence or two is where I'm not clear. Please try again for a dumb cluck. Thanks.