Quick point. Any weapon used in warfare will soon be either reverse-engineered by the enemy, or have a counter developed by the enemy. Actually, probably both. Enemy wizards posing a threat to your siege engines with fireball? Why doesn't that nation enchant their siege weapons with SR, or keep spellcasters around to instantaneously repair the damage? Also, siege weapons have a much greater range than spells, unless the enemy has very powerful wizards, or is spending reasonable amounts of money on metamagic rods. In the first case, the powerful guys have much better things to do than destroy siege engines, like fighting their counterparts in the enemy army. In the second case, what has the other army been doing with their money? They could be buying the same things, but then, if they're protecting/repairing their siege weapons....... the enemy's going to waste some spells.

As for the OP's question, I'd say you could use Heroes of Battle. It has siege engine stats, rules for volley fire, sappers, etc.