I have learned that the first models have an issue with the effects loop. So, I run my pedals infront of the amp. Atleast I try to. I didn't really have an issue until I added in the noise suppressor. I had an issue with the amp for a while where it didn't work (still don't know what was wrong, it's only a year and a half old) but now it works fine. I'm not sure if it's just my bad memory or if the amp actually got noisier.

I use a Boss BCB-60 pedal board.
Guitar>TU-2 >DM-2 delay>TS9>NS-2 >amp.

Just wondering if anyone could help me out. Am I doing something wrong? Not much pedal board experience.
what seems to be the problem exactly?

is the NS2 on battery or AC adapter?

same outlet as the amp and the rest?

do you really need a noise surpressor?

noise surpressor before the amp is usually to block guitar noise
noise surpressor in the loop is usually to block amp noise

maybe try focusing on what is actually causing the noise.
All pedals are powered. No batteries.

Basically my problem is.. The amp is noisy to begin with so I want to eliminate the hum (using a LP, no single coil hum here). When I put the NS2 on the board, the overall volume is low. And this is with the pedals off and on. When I take the NS2 out and run everything else, it's fine. I have the NS-2 after all the effects. So basically, the NS-2 causes a volume drop just with it connected to the board.
I think that is just the way it is.

I had a MXR SmartGate and got rid of it for this reason. It just was not worth it.

If the amp is noisy and there is no Loop then there is not much you can do except tackle the noisy amp (grounding, overly microphonic preamp tube, outlet/house power issue, etc)