Yakima produce a range of kits for different flush roof rails. They all fit in a slightly different way. You'll need to refer to the instructions for the kit you are using. These instructions are supplied with the fitting kit. You can also find them on the 'fitting instructions' tab for the roof bars on our website.
This video shows how you fit K739 but the principle is very similar for most Yakima flush roof rail kits. You may find this video useful, when used in conjunction with the fitting instructions for your roof bars: