In the Set Up,the VP tokens are to be placed in an 'opaque container'. In the scoring the rules state that VP's are awarded, should this be read as 'VP tokens are awarded?'.
No, you draw VP tokens from the container during the regular course of the game by removing Enemy Fleet tokens that are on the board or by playing certain Action cards.
Later, during the scoring phase...
The players now reveal the VP tokens in their possession.
Each player scores VPs equal to the values of their 3 highest value VP tokens.
All VP tokens are placed back into the container at the end of the scoring phase.