I have the Ace rock sliders and they allow you to leave the Rubicon rails on. I think it looks cool with the double stack. My daughter uses them as steps to get in. I'm tall enough to just step in without using them as steps, but they do work that way if you need it.
Mountain Off Road Ent. (MORE) makes a single hide-a-step that should fit under the Rubicon Rock Rails. They're not cheap, but at least you can chose where to install them -- like only on the passenger-side or only for the back doors.