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You name your cells the same as your 3D models.
For SMT parts origin should be center of the pins /pads as 0,0.
Make sure you keep X, Y ,Z and Theta in the same configuration between the 2.
I always took X=as left to right, Y= top to bottom Z =come out of the screen towards you and theta= rotation
Keep a hint map which forces the mapping of model to cell.
In the past we did it without a hintmap as long as the cells/Parts were named the same as the 3d models.
Also note that if you aren't using EDM librarian you cannot automatically map models to your parts, you'll have to map them manually in your 3d layout.
Thanks for the tips