My workflow is the following: I copy my images in one hard drive, having my own folder structure. All these files are backep up regularly on 2 different hard drives.
Once this is done, I import in Aperture library the files: I work, sort them, edit them, create multiple versions etc ... and I have 2 vaults, once updated every day, the second one every Friday.
In total, I have my original files backed up twice (outside aperture library); and I have all my files in Aperture with 2 vaults. Given the low cost / GB of hard drive today, it find it quite workable.