what i sometimes find myself doing, is making the fondant caps.... and letting the dry... dont know if that would work for you...
This is just an idea and I haven't tried it yet: But, you can probably try molding or shaping the fondant into a "hump" before you place it on top of the cupcake. To shape it you need like a round thingy to place the fondant on top for it to set or dry for a bit. Once set or a bit dry you can then place it on top of the cupcake. You probably have to measure and cut your fondant beforehand so that it doesn't go over the cupcake. Hope this helps.
When you make your cupcake, preheat the oven to 400. When you put them in the oven, reduce the temperature to 350. The slight change in temperature helps create the hump because the outer edges cook a bit quicker.