I layer all my mudcakes - and fill with a good layer of a complimentary flavour ganache.
I think it adds to the eating experience and definately helps to keep the cake moist BUT more importantly I think it adds to the structural integrity of a cake - especially if it is carved - think of it as the reinforcement in the steel.
My cakes are normally 4 to 4-1/2inches high completed - so a 3-1/2 to 3-3/4 inch cake with 2 layers of ganache and a ganache undercoat will increase the height - the fondant layer is only about 1/8inch thick
I always bake my cake in total - not split between pans
I collar the 3inch high cake tins - extending by about 2inches - and fill the pan to approx 1inch from top of pan with batter.
I always use homemade baking strips around the cake and cover the top with an alfoil 'tent' for the entire baking process - it creates a level flat top that will not crack or dome.
The baking time will increase substantially so I reduce the oven temp to approx 150-160'C in a fan-forced oven - a 12inch cake can take 4+hours