The ShipCount field determines the number of special ships. There are no guarantees as to exactly what types of ships will show up, but they will always act as a fleet.
Auxiliary ships are not what you need to use. I quote the Pre-Release EV Nova Bible, Revision 7/6/01:
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**The next few fields tell Nova about any auxiliary ships you want to be placed in the universe for this mission. Auxiliary ships cannot be given specific instructions, and no goals can be set for them; they simply are "normal" ships that are placed into the universe for the purpose of adding atmosphere to a mission.
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Auxiliary ships don't really do anything, they're just there. However, you could double the size of your special ship fleet by having 31 special ships (the maximum), and 31 auxiliary ships that are all enemies of the player. Of course, everybody would claim you were a sick, twisted, sadistic, satanic person and immediately demand that you be placed in a padded cell for the remainder of your life for the good of society.
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Suddenly, the little scoutship disappeared and then reappeared right behind the alien warfleet. The gravitic ship's captain hailed the armada. "You are going to be destroyed, but I will give you a choice as to how you want to spend eternity: big pieces, little pieces, or quarks?"
Dead silence.
"Quarks it is, then."