The Aperture library file containing the thumbnail and adjustments history for the images resides on the internal HDD and I keep a copy of it on the external. The referenced images themselves also live on the internal HDD with a mirrored copy on another external. Just for fun I've relocate some of the master images using Aperture and it finds them in the new location no problems - including external.
So, I'm set up as follows:
Internal - working Aperture library and the photos in referenced mode
Ext 1 - Time Machine backup 500GB for all data
Ext 2 - copy of the Aperture library file maintained via The Vault in Aperture plus a duplicate copy of all photos
I end up with 3 copies of all images. Ext 2 is effectively my insurance policy plus overflow. As my iMac isn't going anywhere, I'm not worried about keeping images there.
PS - there aren't individual sidecar files as such in Aperture, just in case that part wasn't clear....