currently there's no multiple device support built into the standard
backup/restore (files are stored under your user ~/Library/iBackup/
However, you can always perform an individual backup where you will
receive an archive (zip) of the backup which then you can put and name
wherever you want (and use those zips for individual restores later).
The ominous RSA key loop (which really isn't anything about key
generation but another problem with the redirected directories that
cydia creates) I need to look into again with the new 4.0 versions
now... I could never really detect what exactly the error causes, so I
need to rework that issue.
Thank you for your compassion!