Manual D is a method of designing ductwork using much of the information you have available off of a Manual J, the selection of equipment from Manual S, and adding a bit to it for a complete design on ductwork. The heat load on the room is a big factor for how much air you need but it doesn't tell the whole story. Types of ductwork, length of ducts, pressures on the house, types of filters, types of units, etc... all play into it. Once all your static pressures and friction rates are figured you have yourself a duct design.
Because Manual D takes into account the static pressure that you want your unit to run at, grill resistance, filter stoppage, etc... it gives you a design that works to operate with your unit at its designed pressure and is more accurate than a simple ductulator with assumptions in all those areas. There will still be times when dampering is necessary but for the most part your rooms will be as close to exactly what they need as possible to maintain what you want your system to run at.