There are lots of options. Use what works for you, keeping in mind that a good marking tool will give you a line you can see, that stays around for as long as you need it, and is completely removable when you're done with it.
Projects that are handled a lot need a marking tool with staying power, others might do well with a line that brushes off.
Whatever tool you use, TEST IT on every single piece of fabric you intend to mark it with before you begin. Can you see the line? Does it last? Can you get it off? Water (ph level, mineral content, additives) varies from town to town and can make a difference. Read product directions.