If you're going to do noise reduction, do it immediately following RAW conversion. I don't do anything special if I think I might do double noise reduction; my goal is to always kill as much noise and as little detail as possible. I usually make a new noise profile for each image; an accurate noise profile seems to be key to effective noise reduction. After Neat Image, I run Focus magic and my sharpening action, do any color correction if necessary (usually not, due to having Camera RAW calibrated to my cameras), curves to adjust tonality, etc. If sharpening brings out too much noise, I'll run a second Neat Image pass making a new noise profile (the sharpening and stuff changes the noise characteristics) and then call it good. I may fade the last Neat Image pass to dial it back if it gets too aggressive.