Casual play

Well, the problem is not how to use PKHEX, I know how to make "legit" pokemon, the problem is how to put my pokemon in the game with the homebrew launcher xD
As Pingouin7 said, get svdt and you'll be able to backup your savefile. It automatically creates a backup at SD:/svdt/<game>/<date>/ when you launch it.
Next, use the built-in microSD transfert tool to access your microSD and copy that "main" file onto your computer (it's best you don't physically take your microSD out each time, as it will damage your back cover on the long run).
Do whatever you want with PKHex, save your new "main" file and put it back on your SD card using the same tool (you can put it wherever you want).
Launch svdt again, search for your edited main and press Y then Select on it to paste it into your cart savefile.