The Blood marking system is applied to the whole deck (except jokers). You need to apply it to every single card. You then need to learn the markings so you can identify the card at a glance. Then you can do the tricks...
The markings are applied before going anywhere with the deck. If you did it during the trick you might get noticed... Once it's done though it's done for good, and if you lose a card it's super easy to just mark another one.