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Preferred Enemy gives you re-rolls when attacking your Preferred Enemy. However, attacks are usually made against a unit rather than a specific model in the unit; hits are only allocated to specific models when rolling saves.

How does it work when you have Preferred Enemy against only part of the target unit? For instance, the attacking model has Preferred Enemy (Space Marines) and is attacking a unit consisting of Astra Militarum faction models with a Space Marine Independent Character joined to them. Does it matter if there is a challenge?

Also, does Hatred work the same way?

 Perfect Organism wrote:
Preferred Enemy gives you re-rolls when attacking your Preferred Enemy. However, attacks are usually made against a unit rather than a specific model in the unit; hits are only allocated to specific models when rolling saves.

How does it work when you have Preferred Enemy against only part of the target unit? For instance, the attacking model has Preferred Enemy (Space Marines) and is attacking a unit consisting of Astra Militarum faction models with a Space Marine Independent Character joined to them. Does it matter if there is a challenge?

Also, does Hatred work the same way?

As far as I know there is no RAW way to resolve this.
FWIW, how we tend to play (and this goes for PE: (unit type) too) is use the original unit. By which I mean, is it a Tactical Squad, Bike Squad, blob Squad? etc.

You have PE Space Marines? Okay, if it's a Guard/AM squad with a Captain in it, you don't get it (barring Precision Shots/strikes that are allocated to the Captain, and challenges of course)

If you're in a challenge, it's quite obvious as to whether that model gets PE or hatred against something by checking the enemy challenger's faction.

An IC attached to the unit is a member for all rules purposes. So you need PE (unit) to have any effect