If you have a custom application which does not have an entry in the Unity launcher you can not launch the application from the launcher and because of that you can not launch it from Gnome Do either.
To add the application to the launcher you can create a applicaitonname.desktop file in ~/.local/share/applications containing the following text:
[Desktop Entry]
Name=Application name goes here
Comment=Comment goes here
Exec=/full/path/to/executable
Terminal=false
Type=Application
Icon=
You need to use the full path to the executable file. A path relative to the home directory does not work. I.e. ~/bin/application should be /home/username/application instead.
You then need to make the file executable by running
chmod +x pathtofile
You can now launch this file from the Unity launcher. You have to restart Gnome Do For it to pick it up correctly.