My suggestion is to consider continuing to use your Honda Fit bike trunk rack for your bikes. This will free up the crossbar space on the roof rack for the luggage box and kayak racks. The ideal setup would be to mount the cargo box on the crossbars in the middle. Then select the j-cradle style kayak racks (either the Yakima BowDown or HullRaiser models) and attach a kayak rack off to each side of the cargo box near the ends of the crossbars. The Yakima SkyBox 16s is a superb cargo box for luggage gear and will complement your 2008 Honda Fit nicely.
MULTI-PURPOSE ROOF RACK SYSTEM
The Yakima Q Towers multi-purpose car rack base system is designed for your 2008 Honda Fit. The Yakima Q Tower complete car rack system includes four Yakima Q Towers, two pairs of Yakima Q5 Clips (these Q Clips are specific to your 2008 Honda Fit) and two cross bars. You can then attach any of the various Yakima roof mount bike, kayak and luggage carriers to the Q Tower front and rear cross bars (see my specific gear carrier recommendation and bar length suggestion above).
Here is a good pic showing the Yakima Q TOwers car rack and a couple of j-cradle style Yakima Hullraiser kayak racks on a Honda Fit. You'll just want to go with the longer 58 inch Yakima bars and then attach the Yakima SkyBox 16s or any other cargo box on the Yakima Q Tower cross bars in between the 2 kayak racks.
http://www.orsracksdirect.com/honda-fit-kayak-roof-rack.html