@matt@sm0g You usually don't start with something like that. You usually start with something fairly standard and then start tinkering with the features as you go, and you eventually end up with something personal that makes sense for you and your workflow.
@matt@sm0g You could have a regular layer for them. Perhaps Caps Lock+1 could activate your Dvorak layout (which could also be your default layer) with all your quirky functions and settings. And then let Caps Lock+2 activate a 'standard' layout with Qwerty.