If you specify embedded arguments, a final EXE will run as if the arguments are really passed to the program. You can specify variables, read more about supported variables here: Variables

For example, you pack notepad.exe, add a virtual file "1.txt" and specify "<BoxedAppVar:ExeFullPath>" 1.txt as an overrided command line. A packed notepad.exe will show 1.txt loaded from a virtual file.