You *could* put the Eclipse into your amp's effects loop AND use its XLR outs to send to the PA on separate channels – but if you mic your guitar amp, then you'll end up getting the Eclipse on all 3 channels and it will be difficult to set the levels.  

If you have on-stage monitors, you could just not send the Eclipse back to your amp, just send its output to the PA and then to your onstage monitors.  That way your amp cabinet is Eclipse-free, but you can still monitor the Eclipse too, and let FOH deal with the house mix.

Here's how my own guitar rig is wired-it took me awhile to come up with this:

Guitars into Boss NS-2 (noise gate) then into instrument input of TC G-system, which has compression and filter section in front of 4 switchable analog effects loops.  The key here is that all 4 effects loops are always sending, and only the effect "return" is switched on/off by the G-system footswitches.

Loop 1 send/return connect to Mesa Triaxis preamp (you could use your amp head).  (as an aside, the second out on the Triaxis goes to "return" on the NS-2 for best noise filtering)

Loop 2 sends a mono signal to the Eclipse Ch.1 analog in.  So when the G-system's Loop 1 is "on" the Eclipse gets the output of the Triaxis.  When Loop 1 is "off" the Eclipse gets a clean guitar signal (+/- compression & filter from G-system).

Loop 3 return gets the "out" from the NS-2, which means it gets the Triaxis output as well when "on" (I have it on for almost every preset).

So after the effects loops of the Gsystem, the Eclipse and the G-system are both running in parallel – both can receive either "dirty" signal from the Triaxis, or "clean" signal straight from the guitar (pre-set selectable).

Stereo outs of both Eclipse and G-system go to a stereo line mixer, hard-panned to L and R outputs which go to 2 separate guitar amplifiers (all clean settings with flat EQs).

Eclipse is set to 100% wet, Triaxis-Eclipse-Gsystem levels are all set within individual presets.  Everybody's on MIDI channel 1 so when I change a patch on the Gsystem footboard, everyone gets the same program change message.  I could have done this with a different MIDI footboard, but I have size 13s and the Gsystem's foot buttons are nice and big (not kidding).

Onstage, I have a single monitor that lets me hear everything in mono, so I lose the stereo onstage but at least I can gauge the mix and either tweek the line mixer, or have my FOH boyz take care of it.  I could probably monitor in stereo but the stage is starting to get crowded.

Hope that helps

– Erik