If your reinforcement stacks have a family member, they're controlled by the AI - otherwise (if they're led by a captain) they wait outside for your command. You control the army that initiates the attack on the campaign map.
The advantage of using a family member is that you can get larger (>20?) units on the field this way; AI seems to often try to suicide your generals, though. I've used a decent amount of reinforcements (mostly to pincer infantry-heavy or light cav AIs) and haven't encountered screwtype's problem, which isn't to say that it can't happen.
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