Adding to the WordPress Theme Customiser?


What is the best practice for adding my own custom choices to the default WordPress customiser?
Is there a plugin or best to add via functions (i'm assuming), do you have any tutorials?

I'm keen to just add a simple checkbox choice.
I have a theme which has 2 versions, a default version and a more colourful version.

So i want the ability for the user to choose via the customiser.
Also once its chosen how you filter each option out within the theme, with conditionals i assume?