If you want to change the original archerytarget01.nif you just have to place the new NIF in the correct place.
Data/Meshes/Clutter/Common/archerytarget01.nif.
You don't need/use the CK for this. If the path is correct, both, the game and the CK will use the new model.
Thanks for the replies guys. I apologize though, I had a typo in my previous post. I DO actually have the file located inside the Meshes folder. The path is exactly that: Data/
Meshes/Clutter/Common/archerytarget01.nif
Still no good. I took a step back and totally removed my custom CK .ESP from the equation all together, hoping the standard archery targets would be effected by my modified NIF (which is flipped 180 degrees upside down). But still no effect in game.
I'll keep searching the web. I must be missing something obvious /palm