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I couldn't quite find what I was looking for with this question. So in the top level assembly I have a skeleton to drive some parts, what is the proper way to reference the skeleton? I don't want to place the same skeleton part inside another assembly then create my parts right? Is the proper way to use copy geometry inside the part/subassembly? I could bypass a copy geometry feature by directly referencing the skeleton if I model inside the top level assembly but I don't like to do that.
At the very least, use a copy geometry feature in your part to select the geometry you want from your skeleton in the context of your assembly.
If you don't want the assembly as a parent to the target part, then make it an external copy geometry (ECG). You just need to be careful about making sure the ECG is located the same as the part is assembled. I typically either use default for both or define a CS for both.
If you want to define what is shared at the skeleton level, create a publish geometry feature in the skeleton and tie your copy geom to it. Then, adding new items to the publish automatically adds them to the target part.