Navigation and Helm systems control a ships movements.
Navigation systems take input from the sensors and scanners to determine where the ship is, and where everything else is in relation to it.
The Navigation systems then use that data to plot courses to allow the ship to go where it needs to without hitting anything along the way. Navigation also feeds the location data of other ships to the Fire Control systems.
Navigation can also be used to track ships and missiles.
Helm takes the course information from the Navigational systems and feeds it to the propulsion systems. Helm is responsible for the actual following of the course by controling speed, when to turn and how much to turn. Helm must also be able to manually adjust to compensate for any emergencies that arise.