Since the Eclipse is a 2 channel through, I will assume you mean toslink optical through of the 2 channel s/pdif variety. If it says through, and not out, I will also assume that it passes the signal unprocessed through the Eclipse so that you could simultaneously send it to another unit.
As far as syncing the devices goes, there really is no such thing is BNC lightpipe like mentioned above. BNC on audio equipment typically denotes wordclock only. Lightpipe denotes audio, usually either 2 channel, 8 channel, or 4 channel for higher sampling rates. Also, devices can be synced ( or clocked ) together through both toslink and through 75 ohm s/pdif, so BNC should not be necessary, although it is usually recommended.
My Eclipse is in my live rack, and I have never paid attention to the digital I/O since it usually pairs up with a large Midas console which has no digital I/O facilities. I am doing a show later today in which I will have both out, so I will take a look, and if I have time, do some testing with my laptop. Hopefully the manual is still in my rack drawer of my FX rack, which will give me something to do today during the inevitable breaks, especially with the rain

(outdoor show)