To kill a skull, it must be hit with a charged shot. It's easy to visually distinguish, cause the charged one is blue (normal is yellow). Charged shots must be obtained from upgrades.
The games doesn't point it out very clearly - to enable the boosts (that you purcheased) you have to press "space". Obviously that works only when you have collected enough energy. This is shown by the energy bar on the right. There, the bar has "levels" that point out IF you have collected enough to received the boost.
 "Tesla8"){kind=icon}