Optimizing the airplane for best cruising altitude and velocity
Are you designing a new airplane? If I understand the question correctly, For a normally aspirated engine, the engine is most efficient when the throttle is fully open at a particular altitude, where it produces approximately 65% -75% power. Therefore the airframe with respect to wing design, angle of incidence etc should be matched to give the best lift/drag ratio at that altitude. You will have to consult with the engine manufacturer to establish what that altitude is. Your choice of propeller is also going to have to be factored.
Then you calculate the fuel reserves accordingly.
Fuel reserves are calculated according to legal requirements of the country in which the airplane is registered and also in which it is operating. This varies according to the type of aircraft and the operation. For instance the minimum legal reserves are different for a passenger jet on a commercial flight, to a single engine airplane being operated on a VFR flight in the private category. Most countries laws are similar but there might be small variations, and they all have to satisfy ICAO standards if the country is an ICAO member state.