ANY effects that boost the signal (distortion...compression, etc...) need to go between the guitar and the amp. Always put the noise reduction last in the signal path. You might try moving the noise reduction to the effects loop...but I suspect that it'd do best right before the amp input.

As for using the effects loop of ANY amplifier...you may find that you need a buffer if you put too many effects into the loop and in some cases some amps just cut the signal enough that the manufacturer should have included input and output controls (their own built-in buffer basically). But you MAY need a buffer if you find that enabling the effects loop (if you are able to do that) actually cuts your signal. The way to check this is to put all effects in bypass mode and switch the loop on and off while playing. If it does drop the signal then you WILL need a buffer.

I suspect that you have been unknowingly using your compressor as a buffer and that's probably where your noise is coming from. Put it in front of the amplifier input and make sure you aren't boosting the signal too much and you should have solved your problem.

If you need any help finding a good buffer if you do in fact need one I am in possession of a wealth of links. Just ask!

Good luck! :)