Yeah, to employ PKHEX you need to have basic knowledge of the Pokémon you want to create (obtainable moves, ability, the location it is found, the trainer's name ID & SID,etc.) This is in order to create a legal Pokémon. Then, you may want to read this guide.
To get to Pokémon to your game you can:
Extract your saved game from the cartridge, the edit it and inject it back.
Get or make a Pokémon file (EKX) and then inject it.
In order to do this, you need to employ certain 3ds exploits and/or dongles (Powersaves, CycloDS, etc.); this depends on your possibilities, but you can start looking here.
This would be the basic start-up.
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