Software techniques 

I watched this video that really helped me with this tool.

First, select similar components and group them together (for example, all the shells in the same group).  If you don't want a component in the simplified model, don't select it at all.

Second, select what you want to happen to this group. Your options are

Once all the components are selected, you can begin to simplify. The simplified 3D model will appear on the right hand side of the screen. Once simplified, save it as a new file. Double check that it has all the components you need with section view.

Replace

Some bolts/nuts are important for thermal analysis purposes, however, their helical threads are still unnecessary. In this case, replace them with a cylinder of the same size. You can use the Replace feature. Select the component you wish to replace, then go to File --> Replace.

Note that all parts of the same name will then be replaced.

Mates may be broken if the replacement parts are not sketched on the same plane as the original parts. If this happens, you can simply remate the components together. 

NX

For STARLab internal use, please refer to the two NX books in the lab.
I have also compiled my notes (NX Notes.zip) in Latex here.  Additionally, the CSA has compiled NX guidlines, uploaded here.