Tuner out to ls2 input/A return for your clean tone.
Send B to comp input, comp output to return B for your comp/affected tone. Ls2 output to the rest of your chain. Put the ls2 in a/b mix mode, adjust volumes of each and away you go.
Ps. I would personally blend the muff too because I find that in dry mode the clean signal is too loud. Therefore put muff in norm mode. Go comp out to muff input, muff effect out to ls2 b return, have the A/clean volume at 10-11 o'Clock and B/affected at 12 o'Clock.
It may seem complicated but once you understand it its rather simple. Enjoy the most important pedal you will ever own.