I just replaced that someone else had done a poor job of replacing before. I didnt change the inners, just the outers.
The end caps simply cap off the end, just seat it flush and you should be good to go. You can use the splash shield holes to help verify the end cap is where its supposed to be before welding it.
The critical part is the area that the fender edge an door edge line up with. There is a triangular notch on the bottom of the inner and outer rockers that you need to make sure line up. They dont always line up completely but should be at least 50% lined up if that makes sense. I looked at many original ones and rarely are they perfectly lined up.