Hair meshes need 2 primary NiTriShapes, named in a specific manner - Hat and NoHat. NoHat is the hair that you see without any helmet/etc on, and Hat is for when you're wearing something that replaces the hair (cap, helmet, etc).
Your best bet is to make a custom Hat NoTriShape, so that you can take your custom hair and reshape it to suit the needs of whatever helmets/hats etc you intend to use.