I Just got a JM4 as well. I use a POD XT (mikes SRV) clean patch with chorus, delay and rev. I like these amps and FX better than the 2.0 spider fx that are on the unit by a long shot. I use a route 66 pedal for overdrive and compresson. That way I get anolog creamy overdrive and a great compressor as well because I am not to fond of L6 digital distortion or the compressor just my taste no offense intended. heres what I do.

Go to the "settings"  hit the button 3 times, scroll down to the auto select settings for the amp, tone and fx section and turn all 3 of them off.

that way when you switch songs it wont keep selecting the amp section and turning on a preset tone after you switched it off.

I also set the mode from normal to preformance. That way the  "amp out" sends only a dry guitar signal to your pod and the L/R line outs send just the jam track or drums to the PA. or whatever your plugging them into. I find I can contol volume better from my PA than having to internaly adjust the levels.

works like a charm. Be sure to turn the level all the way up on the back after you set it in preformance mode to get a strong dry signal to the podxt.

I dont feel it colors my tone much if any, considering of course I am already running my signal through  a pod a route 66 and a Digitech vocalist live 2 LOL!   I run all this into a Bose L1 system and get a great tone in my opinion. I play acoustic pop, blues, classic rock ...etc in a trio in bars about 2 or 3 times a month. so your not talking to a  signed Pro here. Also I am not a huge tone snob who "must run pure tones with true bypass" and all that hype just a guy who plays out and wants to sound the best he can when playing.

it works Great that way  for me.

Your discussion about the JM4 coloring your tone got me thinking ....I unplugged my JM4 from my signal chain and dramatically heard the diffrence.

In my signal chain it dampens my tone and also cuts the signal volume. I unplugged it and everything was crisper and way louder. Just too much gain stageing for me between the JM4, the PODXT and my ROUTE 66 pedal. I like to keep the live setup as simple as I can.

I now run the JM4 as a stand alone practise/recording rig. Thats what its desighned for I think (and by the way what I originaly bought the pedal for.)

Its a great spare PA/rig setup that way. I also love it for creating new loops for upcoming original material. That being said it will not be a component in my "live" rig unless for some reason thats all I am using.