The flies are the "Points" of this game and by collecting them it increases your game highscore, on the top left shows both the number of lives you have and how much points you have gathered.
Halfway through the game you would come across these black and white checkered flags, these are checkpoints. Once the player touched/obtained a checkpoint, they would be sent back to the spot where they touched/obtained the checkpoint every time they lose a life.
At the end of the level you will see a black and purplish portal, this portal will take you to the end of the level. After the end of the level, screen will show your highscore.