CloudEndure run scripts on a target instance after it's launched. This is done by placing scripts in the following folder on the source machine:
Linux: /boot/post_launch (any files that are marked as executable)
Windows: c:\Program Files (x86)\CloudEndure\post_launch (any .exe, .cmd or .bat files)
Once you put these scripts in the above folders on the source machine, the folder will be replicated to the target and be executed once after the target instance boots the first time.