How to calculate the fuselage geometrical parameters?
There is no straight answer or a formula for this one. In real life you first think of what you want to fit inside the fuselage and then design the rest of the plane. For airliners that would be space for passengers and luggage as well. Different fuselage shapes come straight in line from the requirements that the airplane is supposed to meet. Antonov has the shape you described, because it needs a lot of space inside and should stay low to the ground, so it's wings are mounted on top. It also has a huge weight, so a strong set of wheels is required - hence the shape at the bottom (to create enough space for the landing gear to hide without taking the loading space) 

Apart from functional requirements, designing a fuselage must take many different aspects into consideration (starting from the most important - but of course the hierarchy depends on many factors):


mass
drag - the frontal area is not all, it is also the nose shape, wing connection and overal area wchich results in friction loses
stress caused by wing's lift and drag, momentums of wing and stabilizers and pressure difference
fatigue safety
doors, windows, landing gear