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The .Designator ref des string on the overlay layer will appear when the library part is placed on a PCB. You will need to position i. A default position does not help much. If you want a separate assembly drawing then you do need to put the .Designator string on whatever layer you intend for assembly drawing. Typically it is Assembly Text Top or Assembly Top.
Any vias in the center pad will take on the net that the pad gets connected to at the PCB level. This is also true if you put any other copper (tracks or pours) on the footprint in the library.