For sake of argument, let's assume you have an image that needs some noise reduction in some areas and then some sharpening in some areas. The layer structure will probably look something like this:
Some other Adjustment layer
USM applied to a Stamped version of layer stack (with mask to paint in sharpening in selected areas)
Some Adjustment Layer (to mimic you original post)
Noise Reduction (with mask to paint in selected areas)
Background
You will likely want to apply your noise reduction before you start making adjustments and sharpening, because you do not want to accentuate the noise (unless, of course, you do want to accentuate the noise). So, you make a duplicate of the background layer (CMD-J, CTRL-J) and then apply your NR, painting on a mask for this layer to reveal just the NR'ed areas you want.
Once you get your layer stack of the background image plus the layer above it containing the selected areas of noise reduction all set up, you need to make a STAMPED composite of the stack - select the top layer of the stack and hit CMD-OPTION-SHIFT-E (CRTL-ALT-SHIFT-E) - this will place a flattened copy of the layer stack on top of the stack, leaving the stack intact underneath.
This operation merges the good parts of the background with the NR'ed parts of the NR layer - this is what you then want to apply your selective sharpening to - the selectively noise free image. Apply your USM to this stamped layer - you can selectively paint in the sharpening using a mask on this layer, apply adjustment layers on top of the stack, etc.
There are ways to do this with smart objects, but that is beyond the scope of this post.
kirk