You could separate the files you want to backup vs not backup by making them managed vs referenced masters. Which way you separate them is up to you, but the idea is the managed masters would be inside the Aperture library, while the referenced masters are outside the Aperture library (in some arbitrary location of your choosing). The central idea is you can then backup the Aperture library and the referenced masters location using different techniques.
Separation of Photos
If the photos you want to backup are kept as managed (which I'd recommend), you would want to have the online backup of your whole Aperture library. This has the added advantage of backing up any metadata, edits, project info, etc (though comes with the cost of also backing up previews/thumbnails/faces data/whatever).
So it's then just a matter of backing up the Aperture library, e.g. via Aperture's vaults system, Apple's Time Machine (USB or network-share-based), or by putting the Aperture library in Dropbox/Google Drive/etc. Or a more manual solution like rsync or simply uploading your Aperture library somewhere regularly.
If the photos you want to backup are kept as referenced masters, then you could locate them in a Dropbox/Google Drive/etc folder, or otherwise manually/automatically backup the location you put them in, much like the above. Pretty much anything except Aperture's vaults system.
Which way you go (whether important files end up managed or referenced) really depends what you're doing with the photos in Aperture—whether you want to keep the Aperture library info or not.
Moving files between the two
Either way, you can set up Smart Albums to allow you to easily move files from managed to referenced, or vice versa, based on things like metadata/keywords, a star rating, coloured tag or flag state. For example, if you tag the important shots with the 'red' colour label, your Smart Albums would be:
Smart Album 1 (photos to be made managed)
- Match ALL rules, from the whole library
- Color Label is red
- File Status is referenced
Smart Album 2 (photos to be made referenced)
- Match ALL rules, from the whole library
- Color Label is not red
- File Status is managed
Then you just (regularly) check those Smart Albums and change the files between managed/referenced appropriately.
Simple, DIY Off-Site Backup Alternative
Another option that you may find simpler is to just use Aperture's vault system with a couple of external USB hard drives. Keep one near your computer, backup to the vault regularly (after major import/edit sessions). Keep another off-site (at work, at a relative's house) and swap them around occasionally, or take your computer to the other site (if a laptop) and backup there.
I use a mix of both, personally. My important/current working shots are managed, and backed up to a vault at home + another at work. My older/archived shots are referenced masters on a network share (NAS), which I manually backup about once a month. Once the NAS is backed up, I can safely delete the "files removed from Aperture vault" directory beside each of the vaults (On syncing a vault, Aperture moves files out of the vault, rather than deleting them, if they have been removed from the Aperture library or changed to referenced masters).
