Backup your game's save with either svdt or Save_Manager. Copy the save into your PC and load the save through PKHeX.exe. Place the LEGIT Hoopa inside one of your boxes(when you load the save with the program, the first thing you see are the boxes), save the save(it will be a "main" file without any extensions), copy the EDITED save to your sdcard or where the specific save editor reads the saves, and load it up. You can find ALL Legendary Events from the ProjectPokemon forums(there is a dedicated thread with almost ALL LEGIT legendaries). This is how I got Diancie, Hoopa, Shiny Japanese Rayquaza and 3 boxes of events. xD
Protip: keep a backup of your save file to some safe place, because if you screw up with the EDITED save, you might want to restore the UNTOUCHED backup.
Although inejcting a Pokemon into the save won't screw up(if it screws up, you did something wrong), you might be tempted into touching the in-game Legendary flags(all the legendary that are caught in the game) and this might screw the save.
I caught 2 Kyurems because of this; one Adamant and one Modest. xD But some months later, when I edited the flag for Latios(I have Alpha Sapphire so it required an Eon Ticket), the save got screwed and the Delta Episode started again. I did some tests and I found out that touching ANY Legendary-flag screws the game(version 1.4 introduced this bug? I'm not sure) Thankfully, I had sent my save file to a friend of mine so I fixed it. (There were invisible people in the game, and it all happened when I finally got my Gold Trainer ID FML! xD)