Hi,
The Apogee has SpDif and Adat optical and optical Spdif outputs. You should be able to use the regular SpDif out put with all of out products and the optical outputs with the 001, 002, and 002 rack. You just need to connect the appropriate output on the Apogee to the appropriate input on your audio interface and set the correct clock source in the hardware setup. Check out the section of the getting started guide called Recording To and From Digital Devices. You can download a copy at the link below.
http://www.digidesign.com/support/docs/
Thanks,
Digidesign Tech Support