I did exactly that, thanks for the warning; I'll avoid duplicating the files in explorer from now on.
The edit here option in assemblies looks like part of what I need, though I still have questions about setting up relations between parts. Some are a bit off topic so I'll leave them for another post. Here is one example where I was experimenting in assemblies and got geometry referencing working, but also locked the part from moving.
Example 1:
In assembly mode I create a simple part with a slot and hole cut perpendicular along the floor plane. Then I create another part in edit here mode. I offset the front plane, created an axis using the floor plane and offset plane, then created a 45 degree plane based on those two (not sure if there's a simpler way).
After this I just created a thin sheet using this new plane as a sketch plane. So what I want to do now is bore a hole referencing the one in the first part. If I attempt the project to sketch or use any constraints on the angled face/plane I get strange results, ovals or it just doesn't let me do anything. I ended up setting up a sketch on the front plane instead, and it let me project properly while maintaining relations. But now I can't move the part in the assembly any more.
Is there a way to have the objects free and have another shape be booleaned out of them, kind of like how you can set up a boolean modifier on multiple objects in blender and still move things around. eh... not sure if I'm making sense... Trying to learn how geometry can reference itself from part to part basically and best practices. Drilling a hole through multiple parts, referencing features from another part while keeping them 'live', etc.