My reading of the rules is that it would be legal for you to place hard cover when setting up the game. However, the rulebook also recommends that your opponent should then be able to choose which side of the battlefield he will fight from. Alternatively, you and your opponent could follow the alternate placement method given in the rulebook for setting up the game for competitive play.
The rules for target priority in shooting also seem pretty clear to me. If the skirmisher unit behind hard cover is the nearest unit to the missile troops and is capable of charging them, then the missile troops must shoot at the skirmishers as their first priority. One solution would be to move the missile troops out of charge range and utilize them elsewhere, and then use heavier formed infantry to charge the skirmishers in hard cover and drive them away. OTOH, if the missile troops are in a formed unit, the skirmishers cannot charge them, and so the formed missile unit does not have to prioritize them.
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