There is not a way to simply define faces that are used to create the relationships. Instead, you would need to create relationships on the occurrence that represent how the occurrence is to be placed in the assembly. Then, you can call the CaptureRelationships method on the Assembly.Occurrence object. Using the screw as an example, you could create a mate or planar align for the flat face and an axial align to align the screw in the hole. Then, capture those two relationships for the screw occurrence.