When booking flights that involve "change of plane" (one flight number, but change over to another aircraft at an intermediate destination, ex. AA 44 SFO-JFK B767, JFK-CDG B777), the online booking sites can only assign seats for the first leg of the journey.

In theory, is it possible for the airline to assign seats on both sectors (same flight number, different aircraft type)? Or will they have troubles doing so if the agent in incompetent?