If you expend a markerlight token to grant Seeker to the missile, the missile must be fired at the same target as the vehicle's other weapons. One thing to note is that it does not reduce the number of weapons a vehicle can fire at its full Ballistic Skill.
Can you dummy fire the missile? I think some common sense can be applied here. The missiles are located in the forward facing position on the craft. Consider it to be forward facing when resolving the firing arc.
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