Basically AutoRun is executed after AutoCopy. But this only applies on folders that are already on the storage device while booting. The system does not trigger a second run of the scripts after AutoCopy is executed.
I assume you want to start the executable from the target where it is copied to by AutoCopy. In that case you could write a batch script which will be triggered by AutoRun which then executes the binary from the target location. Assuming you have the AutoRun and AutoCopy folders on a USB device, the structure would look like the following:
The .lnk file is necessarily because with older launchers, you can not run .bat files directly. After AutoCopy copied the files to the device, the *.lnk file will trigger the *.bat file. In the batch file you actually execute MyApplication.exe with referencing the fullpath of the binary (i.e. \FlashDiks\MyApplication.exe) .