[Nerfix]

I've never realy had such problems. When using "XYZ Clouds", i either use:
A)Wards(expensive... but can be worth it)
B)Units immune to the effects of the clouds.

Try giving Amulets of Missile Protection to your heroes... I have a funky strategy for Calum that i call the "Arrow Grasshopper". Let's just say that it features Storm General, Bowmen and Amulet of Missile Protection...

"Managing" your troops better might help too... It's not good idead to give archers orders to shoot closest and then have your infantry attack closest too... I usualy order bowmen to shoot at commanders/magic Users.