Leafre Set, All Skills +1

does the two bonuses mean you get both of bonuses for any given set when you complete that set?

Also, do you level up the crusader codex the more cards you get? If so, does anyone know the thresholds needed for each level of the codex?

You get all of the bonuses from whichever set you choose have active. As for leveling the Codex, you must complete sets before you can gain any points toward leveling your book. I don't know the thresholds though.