When importing via iPhoto it displays both "Already Imported" and "New Photos" and defaults to importing just the new photos, although the already imported can be selected if desired. Don't know about Aperture.
Another option you might consider is import all of the photos, delete them all from the Camera Roll and then use iTunes to sync back the ones you want to have on the phone. That way they are all on the computer as a safe storage site that you can include in your regular computer backups. I have an iPhoto Album named "iPhone" with albums inside of that so they are organized on the phone; the photos themselves are in Events in iPhoto.