With the flying fortress' I found it most helpful to cover what I could on the ground first (usually with my creature and a summoned demon or undead). Then when I had to fly, I would try to take out whatever was closest, heal, then change back before anything could kill me. Slowly but surley -as I cleared the ground, I tried to clear the ballista's/nests/lightening/wizard towers in that area to mark it as done. Hope that helps a little when you try again. With Stone himself, I held him for last, went in and leveled up using Raze's fortress (outside), then went back after Stone.
