...the script is a wrapper script for an executable. When the executable runs it shows up with the gray ? icon in the Unity bar, so I end up with two icons (the icon I want and the gray unknown icon). How can I make it so I end up with only one icon (or two equal icons if need be).
There's not much of a way to deal with such thing. Make another
.desktop file for the program that has gray icon and store it in your
Information on how to do so can be found here: Apply icons to bash scripts