The Battle of the Cowshed offers a chance to show Napoleon and Snowball's true mettle as leaders of the glorious revolution. However, during the battle itself, only Snowball participates; Napoleon's name is only mentioned once during this chapter, and only in the context of sending out pigeons to foster dissent in the other farms. Snowball alone is responsible for organizing and leading the counterattack that drives Jones and the other men off the farm for good.
Snowball, who had studied an old book of Julius Caesar's campaigns which he had found in the farmhouse, was in charge of the defensive operations.
The pellets scored bloody streaks along Snowball's back, and a sheep dropped dead. Without halting for an instant, Snowball flung his fifteen stone against Jones's legs.
(Orwell, Animal Farm, msxnet.org)
For the purposes of the chapter, Napoleon is nowhere to be seen, and it can be safely assumed that he is hiding in the barn or the house, trying to avoid any danger. Like most dictators, Napoleon is a coward at heart; he is willing to use military might (the dogs) to force his will on others, but as soon as there is a credible threat against him, Napoleon hides. This shows that while Snowball was committed to the cause, putting himself at risk to help keep the farm free, Napoleon only cares about his own comfort and gratification, and is not willing to risk his own life for the sake of others.