Missile troop order/protection questions

[Micah]

I believe the target is picked randomly if there is no matching unit type in the enemy army (though I believe the choice is going to end up picking the closest unit more often)

As for protecting your archers, just set your melee units to attack fliers or cavalry, depending...probably on hold and attack so they don't run forward and then have to charge back. This probably isn't 100% effective, but should work decently enough.