By the front and rear arches, the sills bolt to the fenders with vertical bolts, under the door, the sills are attached with L shaped brackets.
The factory side steps attach in 3 locations. First, at the large nut on the bulhead mounting bolt (at the end of the bulkhead outrigger). Second, onto the upright at the end of the tubular outrigger behind the front door (the hole here is large and square and requires a spacer piece to fill the hole and provide a mounting surface - there are 2 bolts here). Lastly, there is a short bracket that bolts to the rear of the bulkhead crossmember and the step so that it doesnt "roll under" when you put weight on it.
If the mounting is confusing you, then you're probably missing a couple little pieces of hardware. No bother really, they can easily be made with a trip to home depot for some metal and a few minutes cutting. Very simple shapes.
Heres a good picture of the rear mount. The front one is not so good since the bolt is pulled out, the running board is hanging, and you cant see the little stabilization piece very well, but its all I've got.