An orphan mesh is a mesh that has no geometry associated with it. You can create an orphan mesh in a couple of ways:
1. You import from an existing ABAQUS inp or odb. When you import you only get the nodes/elements (no geometry, hence orphan)
2. You have meshed some geometry in CAE then you choose "Mesh-Create Mesh Part". This as the name suggests, creates a new part which is a copy of the nodes/elements (but not geometry).
So to your question: you only need to instance one or the other in the assembly. If you decide to, you can use "Instance-Replace" to swap the original "native" geometry part with the new "orphan" part. Loads/BC's etc will be applied to whatever you have in the assembly.
Finally, it is quite valid to mix orphan parts and native parts in the same assembly - CAE makes no restrictions on this. You can then have contact (etc) between such instances...
Hope this helps!