You may have already tried this, but I've often found the simplest answer is just to crank the fuzz or synth pedal's volume so that it is much louder than your clean tone.
When practicing or playing around at home it seems to make the most sense to have pedals set to unity gain. But in a mix a substantial volume boost really helps. My fuzz settings seem WAY too loud when playing alone but I've found that's what is needed for a band setting.
Just my two cents.
+1.
If you're playing with fuzz and there's OD guitar or whatnot, the similar nature of the audio waveforms will blend together and you'll be able to pick out individual sounds less (IIRC). Volume boost helps suppliment this issue. Being able to blend clean with OD is nice, and a feature I use standard on my EHX Bass Muff Pi.