A pilot's den is considered the brain of a Leviathan's biology. Though Leviathans can and do function without Pilots, they are used most commonly on ships that will sustain a crew to increase efficiency of communication and if any problems arise.
Through the Pilot, commands can be given both ways from the crew to Moya, in times when certain supplies are needed, or from Moya to the crew, when an unknown object appears on her sensors.
When the Peacekeepers attempted to create a Leviathan/Peacekeeper hybrid, they attempted to 'breed out' the gene sequence responsible for the Pilot's den, but they were unable to do so. The closest they came to this goal was reducing the Pilot's Den to a vestigual organ- Crichton compared it to an appendix-, with Bialar Crais otherwise remaining in control through a neural link, although Stark was once able to use the den to bond with Talyn when he was being drawn towards a star generating unusual radiation that had disrupted Talyn's usual sensors.