Seems you got it kinda figured out here, but I'll toss in a few cents anyhow...
The NS-2 is pretty much designed to kill feedback and/or little bits of noise you make when you don't want ANY signal to be amplified.
Sure, you can use it to get rid of preamp hiss, but in doing so you severely limit its effectiveness.
When used properly (as in, plug yer guitar into the NS-2, then plug the output into your first effect, amp, or whatever) it gives you ZERO tone coloration. I was floored when I first tried it, and there's no way I'll ever play without one again. The guitar sounds EXACTLY the same with the pedal in or out of the loop, or connected/disconnected from the entire rig. The only difference? No clunks between songs. No feedback when you stop dead on a big fatty palm-muted chord while standing right next to yer amp...
To get rid of your amp hiss, you really should look into a Hush unit. Admittedly, some of the older ones suck big time, but the new ones (such as the one in my Intellifex or the Super C) don't color your tone and quiet the noise floor to an undetectible level. The MP1 doesn't make nearly the amount of noise as my 5150 II, so you should have no trouble getting clear, unaltered tone out of one.
At this point, the only noise I'm getting out of my rig is a low DC hum from the stinkin' BBE... (if you know how to fix it, short of tryin' a whole new BBE, please find the other thread I'm about to start...)
Hope some of that was useful.