are you just trying to convert optical to coax? going thru the atari to do that is a bit overkill. however, you can try using the "monitor" function in cubase. This will route the input to the output of the dsp port. In the audio/hardware settings make sure to select ADAT 1/2 as your input. also, I believe you should have matrix.prg in the auto folder. by monitoring the input (adat 1/2) cubase will route out channel 1/2 of the dsp/external connector which should correspond to the spdif output. are you using FDI or Compo SPDIFS? these are the ones i am familiar with.
that said, you can purchase an SPDIF optical->coax convert for less than $50. check google.