I am adding 2 rooms to my home. I have a forced air AC/Gas Furnace system that uses flexible ducts. They are lying on top of my joists and insulation. I read somewhere that they should be hung up. Should I do my 2 new rooms hung up? Why?

I wouldn't know why. It would be a real pain, putting in a support every few feet. If the original builder got away with it, I would chance it unless somebody comes up with a good reason.