Two of them can also be found in the storage within Lifepod 5 at the start of the game.
Flares can be ignited and thrown by selecting it from the toolbar and pressing the right mouse button. This will cause the player to throw the Flare slightly forward, and then it will sink until it hits another object.
The player can also pick up a Flare after it has been ignited. The ignited Flare stays lit when in the players hand, illuminating an area around the player.
The Flare will not despawn. Because of this, the player can regularly throw a Flare when exploring an intricate cave system. If the player needs to leave they can simply follow the trail of Flares back to safety.