The rules for the flare cards are specified in sections 4 and 5 under 'Setup' of the FFG rules:
Cosmic Encounter Rulebook wrote:
4. Choose Aliens: Shuffle the flare cards and deal two to each
5. Prepare Flares: The flares dealt to each player are then
taken and added to the cosmic deck. If there are fewer than
five players, extra flares are randomly added to bring the
total in the deck to 10 flares. Shuffle the deck.