Are you running the noise suppressor in the loop, or in front of the amp? It won't do much in front because the high gain then comes afterwards.
If you use it in the loop and you can't set it so it cuts off then noise enough because it interferes with the note attack and tail-off, I think you can run it like this: guitar > NS-2 input; NS-2 send > amp input; amp FX send > NS-2 return; NS-2 output > amp FX return, ie putting the amp's preamp in the NS-2's loop. I haven't tried this though, it's a long time since I used a noise suppressor. You would have to put your other effects between the amp and the NS-2 in both loops. This is getting really complicated though, and could potentially cause ground loop issues as well.
If that doesn't work I think you may just have to do it manually as volatileNoise said...