Can I control what I target?
You cannot. When a battle starts, it will scan your opponent’s base and tag the building(s) that the missiles will damage. You begin with just one missile to fire, but will be able to increase the number of targets with Library and University research.

How many times can I fire the Missile Silo?
You can only push the big red button once per battle - provided that you filled your Missile Silo with the required Oil beforehand.
Why can’t I launch a Missile as the first part of my attack?
The Missile Silo, whether on offense or defense needs time to arm itself. You can tap the big red button any time after the 10 second countdown has ended.

Why will it target things like Walls in the Single Player campaign?
Because there are only a limited number of buildings in maps like the Fertile Crescent, The Offensive Missile Silo may target Walls instead of buildings. Missile Silos never target Walls in multiplayer.