Designing the Layout
The layout, in this context, is the physical configuration of the keys on your keyboard–not to be confused with the keymap, which is the firmware configuration.
Unfortunately, planning your keyboard layout is kinda a one-time thing, so you should definitely spend a good bit of time on this step.
Tools
There are several options in terms of tools for planning your keyboard layout, but the one that I have used (and recommend), is Keyboard Layout Editor.
Other Tools