i don't use ghee at all. i tried it once in base and it was way off my taste buds. i now use a little marg in base (came up in the ashoka base) and find it's suits my taste buds.
i think some members add a little to the main dish towards the end of cooking. i would not personally full stop (unless the recipe specifically calls for it ie butter chicken - although i actually use marg in this too).