As you know, normally there are no relative paths in Windows-Shortcuts. But there's a simple way to get it.

To do so, follow the following instructions:

1. Create a normal shortcut in that folder where Deployment Tool and setup files are.
2. In the Wizard type the following path: %comspec% /C my.exe /parameter value

   Example1: %comspec% /C  \subfolder\some.exe
   Example2: %comspec% /C  ..\prefolder\some.exe
   Example3: %comspec% /C  notepad.exe testfile.txt

3. Edit the shortcut and remove the text (path) from the "Start In" field
4. You now have a shortcut with relative path. Maybe you change the shortcut icon to something that fits your needs.