Mixing Ghee with Other Ingredients
There's two methods for this, which can also be combined.

The first, as several people have mentioned, is to make sure that the eggs and water are slightly above room temperature.  At 27C/80F ghee (and, for that matter, butter) is liquid, so if you can ensure that the rest of the batter is that temperature, it will stay liquid when mixed.  The easiest way to do this is to heat the water (to, say, 35C).  Make sure to let the ghee cool a bit before adding, though, otherwise you may cook the eggs.

The second method is the one used for French sweet crepes, where you must add melted butter to a cold batter.  In this method, you rapidly agitate the batter (using a whisk or a blender) while pouring the butter in, in a thin stream.  The butter still solidifies, but it hardens into tiny pieces which are well distributed in the batter.