If you mean the Stratospheric Citadels, he protects them with spells--spells which are separate from his spellcasting every 4 turns. In my current game, I am literally wasting turns--he doublecast Firestorm on one of the Citadels, which means I have to wait approximately 8 turns to do anything to it.
As of a recent version he doesn't pick Firestorm if he's doing an "automatic citadel-protection" cast. He still can during his normal casts, but he doesn't specifically target citadels with those.
Also, those area debuffs cannot "stack": he could theoretically cast 2 firestorms near each other, but it a cast can only affect tiles that do not have any area debuffs currently on them at the time, and it only sets the "turns left on debuff" counter on each newly-affected tile to the length of the spell; it does not add the length of the spell to that counter. Have you seen clear evidence of it "stacking" the durations somehow?
Anyway, glad to hear he's being a suitable pain in the rear, that's
myhis job