>So the digital i/o is primarily used for one external device into the eclipse and another device out >(such as a recorder)?
Not necessarily. As I said it really depends on the hardware (and software) to which the unit is connected. It's quite usual to use these machines in full digital domain. In case you have problems, you could convert only one time, by using digital input and analog output. Consider that Eclipse converters are quite good, surely at the same level as a 700/1000$ audio interface.
Try clocking the Eclipse from W.C. instead than thru digital audio. That should easily keep the whole signal in digital domain.