The destination directory is the destination location for the application you wish to deploy.   If this is an application that's already installed, uncheck "Copy program to destination location" and click Install.

Let's assume you have ObjectDesktop installed on your E: drive when you booted from your D: drive. Now, you installed eCS on your Q: drive.  So, what do you do to get ObjectDesktop working? You drag-n-drop ObjectDesktop to your E: drive, uncheck the copy source file, set Destination to the location of the existing copy of ObjectDesktop, and click on install. Again, you might have to reboot your computer before using Object Desktop.