If this NS-2 is working properly you shouldn't get anything when it kicks in. Maybe a little amp noise but their is nothing you can do about that. If the clipping is happening up front then turn the threshold down so that the expanders take out just the noise not the signal.

One thing to look for is wether their is one pedal (like an EQ, the GE7 is notorious) that is causing all the noise. if there is you may want to think about replacing it either with another brand or getting rid completely.