from what i read,it seems that this is your first quality effect processor…GOOD CHOICE!!!
but you have to spend some time learning some things(internet search is a good start).
the Eclipse have a relay bypass,but from what i understand from what you have wrote, the problem isn't there…
1)for such units,always use a mixer!
the Eclipse may have stellar converters,but with a mixer that will help you keep your dry signal in parallel to effect processors,you will keep the dynamics and tone of your preamp(you wrote fx-loop right?)
2)yes,you can use the Eclipse in mono,but since the algorithms are in stereo…you lose all the magic!
AND…you have two ears 😉
i suggest you to search the forums and to read on how people use a mixer at a guitar rig.