This photo shows the towers attached to the OEM rails and the OEM cross bars are underneath the the new cross bars. the added height provides more room to attach the clamps without scratching the roof.
I keep the OEM cross bars attached so when the box is not used I can put soft bags on the roof between the Yakima cross bars and that bags will rest on top of the OEM bars and be straped to the Yakima bars.
You will need to purchase a Yakima wind fairing to reduce wind noise when the box its not attached. This is around 70 bucks.