Changing package directories

Simply i want to know how to change the way UE4 package the game , i mean they way it creates the folders and place .exe in Binaries\Win64 and package in \Content\Paks , what i i want to change this , how i do it ?

Another thing how would i update my game , instead os asking my clients to download the whole game again ?(like in online games) Can this be done in UE4 ?
Thanks and best regards,
Trice