Yes, you place these as NEW ships in addition to anything else out there. No rules refernce the card says "place" which implies new pieces.
The rules state that you are limited by the components you have. If you should ever need to place ships and don't have enough, then the Current Player decides which of the ships are placed where and what remains "empty."
page 28 of the rules:
Whenever a deck of cards runs out, the current player
shuffles the appropriate discard pile to form a new deck. This
includes Skill Cards, Quorum Cards, Crisis Cards, Super Crisis
Cards, and Destination Cards.
Tokens and plastic ships are limited to the quantity provided,
and can run out during the game. The current player always
decides the order in which a component type is placed, and if
there are not enough, he decides which ones are not placed.
Example: A Cylon attack Crisis Card is drawn that requires
two basestars to be placed on the game board. There is
already one basestar on the game board, so there is only one
more that can be placed. The current player decides which of
the two basestars listed on the Cylon attack card to place on
the game board.
If all vipers are already in play and a player wishes to activate
the “Hangar Deck” location, he may choose to move a viper
from any space area to the “Reserves” so that he may pilot it.