The Manta is a unique vehicle, because it is the only one with the ability to jump. While riding in the manta simply press the jump button and it will fly up. The only time you can jump while in the vehicle is when you are on some type of surface and when the gauge is full.
A Manta's primary fire are small purple plasma shots coming from two firing mechanisms located at the bottom front of the vehicle. Its secondary fire is not dangerous at all, unless there is someone underneath the manta itself. Because its secondary fire is just a boost that sends it to the ground quickly. Holding this button down keep the manta grounded but you still have the ability to fly. this method is very useful in 'decapitating' your opponents.