Some of my items have bonuses. How does that work?

Bonuses will only be available when the associated item is equipped on either your hero or one of your allies.
That section makes no sense at the moment. Are you saying that equipment which has bonuses on it must be equipped by your army/allies in order for you to receives those bonuses? If so, if you auto sort your stuff, will the game prioritize bonuses over raw stats?

Too vague at the moment.