If you're only mixing and not tracking through the Eclipse, and have the Eclipse connected via SPDIF, the mix and resultant effects won't pass through any converters, instead remaining digital from your DAW, through your interface, through the Eclipse, and back to your DAW. Converters are only necessary when converting the digital signal from the DAW to an analog signal. Since the Eclipse, when connected via SPDIF processes the digitial signal directly, it never requires an analog signal and so no conversion is necessary.
Only if you were using the analog ins and outs on the Eclipse would conversion be necessary, and in that case, I agree, the converters in the Apogee may sound better to your ears than the converters in the FastTrack. However, the converters in the Eclipse are also very good, so I wouldn't eliminate them from contention.