You should start with a brief sketch of the instrument. It makes sense to purchase all the material, before you make a detailed drawing in a 1:1 scale. It is easy to change the design according to the hardware, but it is difficult to find materials, which match your design. For example, the headstock thickness of 16 mm (see side view below) was designed according to the gearbox size of the tuners. A headstock thickness of 12 mm would be stable enough, but it would be difficult to find tuners with smaller gearboxes.

You can make your drawing on paper, or use a Computer-Aided-Design-System. A 2D-System is good enough. You will also find some freeware in the Internet, if you prefer to design your instrument on a computer.

It is important to draw the instrument in two perspectives: top view and side view (see example below, click for full view). Write all important dimensions in your drawing. In this early phase it is already very important to think about the feasibility of your design. To give you an example: The radius from the neck to the headstock in the drawing below (top view) is 30 mm (=1.2 inches). It could also be designed with 1.0 inch, or 1.5 inches, but I use a sanding cylinder with a 1.2 inches radius in a drilling machine. This makes it very easy for me to create this radius.