Like OldManModeler said; and also depends on the position variability: is it a part like a figure arm that needs to be rotated to the right spot (where I have drilled and inserted a tight fitting pin to hold it), or a part that needs to be centered or aligned (where I might lightly score the reference piece at the exact spot).
The worst is when there are no features like a dimple or notch to register one piece with another: a common situation with resin kits!