There are 4 types of cards, each are treated differently, and behave differently:
1) Opp ship cards: These are single-sided, and every card is an Opp ship. The back of the card says the name of the Opp. There are in play, face down. When an Opp Ship card is scrapped, it is put on the bottom of the Opp ship card deck. If you go through the cards enough, and you have a good memory, you can know what is coming next.
2) Opp Mission cards:These cards are double-sided. On the top of the front it will say what Opp it belongs to as well as the word "front." The back of the card can vary drastiaclly in what type of card it is. These cards are put aside face-up, you will know what the next mission card will be. When an Opp Mission card is scrapped, put it on the bottom of the Opp Mission deck.
3) Station cards: These cards are double-sided. One side is blue (the SF side), on side is red the Opp side (orange). The SF side can either be a Tech of Boost, the Opp side is either a Boost or Ship (these are considered Opp ships). At the start of the game, 5 Station cards are put in each spot of each Sector. These cards are SF (blue) side up, you can see what you are buying. All cards that were not put in play during setup form the Station Scrap, Opp side up. When a Station card is scrapped (it doesn't matter from where), you put it on the top of the Station Scrap, Opp side up. If a spot on a Sector ran out of cards, you shuffle the Station Scrap, and deal five cards into the empty spot.
4) Strike Force Cards: These cards are single sided (green), with the name of the SF ship on the back. When these cards are scrapped, they are removed from the game, unless the card explicitily says otherwise. Be very careful, many SF ships have a key Tech, and if it is scrapped, there is no way to get it back. During setup, you will put the SF deck into play face up.
The Opp ship and Mission cards have their own deck. However, as the game progresses, your SF deck will consist of Strike Force cards and Station cards. This deck is always face up, so you will see a blue or green card, as opposed to a SF back or red card.