Runes are used for a few things in Blood Magic and are a key component when it comes to your Blood Altar. These runes are only used to upgrade your Blood Altar, each rune modifies your Altar in a different way. Think of runes as a way to customise your Altar to your own needs.
As you only have access to the first tier of the Blood Altar and Blood Orb you will only be able to craft a few of the many runes. These runes are crafted with the Blood Orb, don't panic, you will get the blood orb back and it has no durability.
Before you can craft any runes you will need to craft a few Blank Slates, you can craft these by right-clicking Stone into the Blood Altar. In order for this craft to be successful, there has to be a minimum of 1000 LP in your Altar. These slates don't take long to craft and you will need a total of 16 in order to make 8 Blank Runes.
You can also use the Blank runes to craft Speed runes. Crafting things and filling your Blood Orb will be 20% faster (40 > 48 > 56 > 64 > ETC) for each speed rune making up the base of the Blood Altar.