You have to complete each wave before more ships appear. After you complete each wave in a timely fashion you're presented with a screen to choose your power-up and then you earn your bonus points. You should choose 12:00, 3:00 and then 9:00 (which gives you triple bullets). You will not necessarily be stuck with the third power-up for the rest of the game because it is possible to complete that wave before more ships appear and you'll again be presented with the power-up screen.