I was under some major limitations when it came to deploying my troops for that battle. First off, I really did fill the flying ship-- it has a size limit on the troops you can bring on it, and I indeed hit it. Secondly, since all the troops had to be under one commander, I only had the 5 squad groups to set up orders to. The 'logic' behind my deployment was that I wanted the boulder throwers to go in first, fire off their 5 boulders, and then be backed up by the naiad warriors in order to hold the front line while the mages did stuff, and have the earth elementals come in last to do mop-up duty and pierce the remnants of the line. Tien Chi taught me awhile back that Earth Elementals do not tend to survive rushing into a wave of troops large enough that they are still heavily surrounded when the enemy's turn comes around-- so sending them in first would have been a waste. What I did not expect, and what I am still questioning the value of, is the fact that the earth elementals actually hugged the back of the line in such a way that it stopped my boulder throwers from being able to retreat-- many of them were routing but trapped for several rounds.
I guess if I had to script it all again I'd move most of my forces down a bit and then put the earth elementals top-mid with an attack rear command so that they'd participate but not by surrounded and destroyed in the center.
That cockatrace mob actually did more than just break up the line-- it ate a whole slew of boulders and it caused some friendly fire damage. My queen of lakes actually took 30 damage during that round from stray boulders hitting her-- nearly half her health. (which she, being the queen of lakes, instantly regened, but still it represented the most danger she was in for the entire battle)
I did of course expect that my side would rout. That was the whole reason behind the beach landing in what I now understand is the least populated province in the game-- I needed to give my army a place to retreat to or everything would have died from the rout.