In most traditional culinary preparations, you should remove the tough, dark green leaves and just use the light green and white bulb. The dark green section tends to be much tougher and more bitter, which is why it's often not used. (However, you can use it in homemade vegetable broth!) That being said, it's not unsafe to eat the dark green section – it just needs a little extra cooking time to soften. If you decide to use it, you'll just need to sauté the leeks for longer (probably 15+ minutes).