Best place to put Boss NS-2 pedal? And how to effectively use it?

First, why do you have both a Boss Metal Core pedal AND an Ibanez Tubescreamer in your chain? I would think the ML-2 would give you plenty of gain on its own.

In fact, if you cut the Tubescreamer out, you probably wouldn't even NEED a noise suppressor.

As for the actual answer to your question: get a couple 1 foot long cables and put the NS-2 in your amp's effects loop. Then just set it on top of your amp and leave it on all the time.

Also, I like to put my wah pedal AFTER my distortion in my effects chain. I just like the sound better.

There is, in my experience, no problem having more than one overdrive/distortion pedal in your set up. Many players have several for different types of effects. However, using more than one at the same time can absolutely give you lots of hiss and unwanted noise.

If you can't have the noise suppressor connected to the effects loop (if your amp don't have one), or you like it together with your other pedals, you want it at the end of your signal chain, before the amp input (just like you have). You will then need to tweak the settings on the pedal to find what works best for you - enough to remove unwanted hiss and other forms of noise, but not too high to chop off notes and the sustain.

Please be aware that a noise suppressor won't remove all types of noise you may encounter in a guitar rig. If you have mains cycle hum, ground loops or similar issues, you can't eliminate any of that by adding a noise suppressor.