Spaceship customization is fairly straightforward. Basically you choose a hull type (Corvette, transport, destroyer, cruiser, battleship, dreadnaught... I'm not sure if there's more but usually by the time dreadnaughts are unlocked I've won the game), each of which have a certain amount of space/weight and special bonuses for certain types of modules (defenses, weapons, support, etc.). Then you select what modules you want on each ship hull.
You aren't really regulated by anything though right now other than the tonnage of the stuff you put on, so you can have a ship with nothing but weapons, nothing but defenses, support, etc. It allows for a variety of custom ships, but at the same time since there's only better versions of the three weapons and three defenses (rock, paper, scissors), there's not a 'true variety' of ships like there is in, say, Sword of the Stars II. Each race has a single ship model for each class. Mods will probably help this out though.
The cards in battle supplement your ship's attack and defense strength during the three battle phases (long range, medium range, short range). You choose a card that symbolizes your strategy although you have to make sure you have the ships to properly execute it, aka using the "Deflector" defense card if your ships have no kinetic defense will not help you one bit. Basically you should be playing cards that support your ship's strengths or exploiting the enemy's weaknesses. Also remember that each card can "counter" another card type. If your card matches up (counters) the enemy's card, then you will get a bonus to your attack and he will get a penalty.
Playing the "Camoflauge" card (gives missile defense but lowers kinetic weapon dmg) during the first round (when missiles are the most effective) when you're playing a missile heavy fleet is usually a good idea. Of course it's an obvious card to play so your opponent might play a card to specifically counter the camoflauge card.
That was probably more long-winded than it needed to be, but yeah. My initial "ehhh" for combat and ship design has been mitigated by how fun the game actually is.