Looks like you only have jpeg files and not raw files? The problem with jpeg files is artifacts from jpeg compression make it nearly impossible to detect where the sky ends and the horizon begins. The skyfill app is expecting very smooth color transitions from one small group of pixels to the next as it works its way down to the horizon. When it sees a large enough change in color over a given threshold, it flags that spot as "end of sky".
Given what you have shown here, I suggest you go directly to the tutorial. Read the first and second parts (first part is pretty quick). Full sky replacement mode is the second part, and in that mode skyfill gives every pixel a probability of being sky. When it replaces pixel colors it will use that probability to determine how much of the pixel's color to change toward the modelled sky color at that location. You create a text file that tells sky fill how far "down" to proceed re-coloring pixels. The text file just lists line segments in image coordinates.
*You have to be careful and make sure skyfill is not using non-sky areas like clouds or water for sample points to create the sky color model* -- skyfill will make some attempt to throw out bad sample points but it can only do that if the bad points are the exceptional cases. Running skyfill with the "-d3" flag is your friend here.