All of those methods are just as good as the other. The key is to approach the task in a relaxed manner where you feel good, grounded, peaceful and that the crystal is clean first (bury in dirt or sand, visualize cleansing light or energy, wash with water or saltwater (some crystals can't have contact with either or both of those but qz is fine), run through smoke...what feels right for you?). What works for you? You may also try setting up an altar of sorts and placing the crystal amongst objects representing what you want to program it with, or on a piece of paper with a word or intention. You can also just hold it and declare, "Thank you Crystal for being my partner in my intention. I program you with _____. It is done!" or whatever works for you. You can't really do it wrong, so don't worry about that. What feels natural to you? Gravitate toward a method that fits into your natural inclination. Don't feel like you need to do something that isn't fitting into your natural routine or way of life, because you then may resent or feel uncomfortable with the process and won't be inclined to do it again. That said, you can also stretch your comfort zone and learn new things. Remember to only set intentions that can be applied to the good of all (never anything having to do with violating the free will or best fate of others, or for ultimately selfish reasons). You can always cleanse and reprogram it if you so choose. Just like you can erase and re-format a hard drive