My machine (HandiQuilter Amara) only has the vertical thread holder. A horizontal pin is an option.
Cones (vertical) and spools (horizontal) are wound differently, and yes, you need to have the thread come off the top if you're using a cone or you will get breakage (the thread will twist on itself).
Since the longarm head moves, you can't use a stationary thread stand. Have you found a Facebook group for your machine where you might ask about rigging up a vertical holder?