It is important that you loop your effects through the FX loop in your amp. What it does is put your effects right after the preamp circuit, and before the amps reverb.
Even if you go through the clean channel with a boss distortion pedal, it will sound clearer. The order of comp/eq/modulations does make a difference. I recommend this setup.

<--to FX LOOP send (to input)- {compressor} - {eq} - {DISTORTION} - {Chorus/flanger) - (Delay) - (reverb) (output of pedal)-->to FX LOOP return

I hope this helps you out.