In the terminal, to start Jekyll, navigate to your sites root folder and type
jekyll build --watch. The root folder will be generated into ./_site and watched for changes with auto-regeneration enabled.
After you add your project to CodeKit, click on the gear under your project name to access your project settings.
Click the Browser Refreshing option.
_site folder as the Document-Root Subpath:
Set Refresh Delay to more than 0 seconds, I used the preset interval of 0.25 seconds. At 0 seconds, your markdown files will not reload initially. Adding this delay allows them time to build.