In an assembly, you can set the Component Reference for each part.

See 2016 SOLIDWORKS Help - Component Properties Dialog Box

How can I move, copy or dissolve components with "Component Reference" to another assembly while maintaining the "Component Reference" Tag to be used in drawings?

I use these reference tags in PCB restriction drawings to identify the components in the BOM. They correspond with the electrical engineers documentation for layout.

I create the first assembly manually, and give it to the EE for the first restriction drawing for component layout.

When done, he gives me an emn file that I import to Circuit works, and build a new assy.

I place the new assembly into my original assembly, and dissolve the new assembly. Thus, placing the part locations in my original assembly, and update my drawing.

I don't use the newly created assembly because there are multiple display states that I would need to add and I have templates that layout in a specific hierarchy and organization.

In many cases, I also make all the components virtual when I'm done.

PCB/Restriction Drawing Level

Assembled Board Level:

If mechanical features such as heat sinks are added, one more assy level: