What is the exact error message that you are seeing?
SkylineRunner.exe looks through the user's Start Menu in order to find the shortcut to Skyline.exe.
If SkylineRunner.exe cannot find Skyline.exe, then you get an error message that starts with "Error: Unable to find Skyline program at any of the following locations:"
If SkylineRunner.exe can find Skyline.exe, but something goes wrong when SkylineRunner.exe tries to run Skyline.exe, then you get an error message that starts with "Error: Could not connect to Skyline."
Note that SkylineRunner.exe should only be used if you do not know where Skyline.exe is installed. SkylineRunner.exe looks through in the user's home directory for either "AppData\Roaming\Microsoft\Windows\Start Menu\Programs\MacCoss Lab, UW\Skyline.appref-ms" or "AppData\Roaming\Microsoft\Windows\Start Menu\Programs\Skyline\Skyline.appref-ms".
If you actually know where Skyline.exe is on the computer, then you should run the program "SkylineCmd.exe".
SkylineCmd.exe always looks for Skyline.exe in the same folder as itself.
If you want to include Skyline itself as part of your installer, you might find the Skyline Administrator Installer to be helpful:
Also, the "unplugged" installer might be helpful: