Looking for a recipe from scratch for  Chocolate Amaretto Cupcakes.

AYou would used your chocolate cake recipe and add amaretto flavor or liquer.

Thanks, do I decrease other liquid in the recipe such as milk 

AIf you add only a small amount, You don't need to alter the recipe. To enhance the flavor (& the moistness) if the cake even more, you can brush the baked cake with an amaretto cake syrup.

I'd do the chocolate cupcake, brush it with straight amaretto, and then add amaretto to the icing as well.  It's a really delicate flavor so you might want to find a more mild chocolate recipe or make the icing strong.