I think that I have finally determined a solution that works for the sites I maintain. This seems to solve almost all the problems that I have encountered:

1. Install the non-ssl site in the sites directory: nonsecure.example.com
2. Create a new directory in /sites/ for the ssl site: secure.example.com
3. Copy the settings file from the nonsecure to the secure directory. Change the base_url to be the secure site's URL
4. Create symlinks FROM the nonsecure directory to the secure directory:
5. ln -s nonsecure.example.com/themes secure.example.com/
6. ln -s nonsecure.example.com/files secure.example.com/
7. ln -s nonsecure.example.com/modules secure.example.com/