If you right-click on the FX icon in the layers tab it'll bring up a menu. Third from the bottom is an option called "Create Layers". That will convert your Bevel/Emboss into a pair of layers, one for your highlight and one for your shadow. The new layers will retain all of the properties you set in the effects panel including colour and blending mode and will look identical to their original counterparts, but now will be completely editable. This will allow you to add noise manually to the shadows and highlights using filters or custom brushes, or even new layer effects.

It's a bit of a tricky way of working with it but it will give you the control you need.