I think Manaphy is method 1 because it's a gift. Sorry, but I don't remember stuff like that. I always look things up before an RNG project, even if I did it before. Most everything you need to find is on the first page of the help thread.
To get it shiny, you must use the SID and OT of a second game. Then you trade the egg to the second game, where it will hatch shiny. It cannot ever hatch shiny on the game that receives the egg. There's a code to stop it, but the code doesn't work on a second game that receives the egg from the first. All shiny manaphy must have link trade in the description for this reason, but it will still be treated as a hack on GTS and for wifi battle recording, despite that it was gotten legitimately in the game.
To get it shiny, you must use the SID and OT of a second game. Then you trade the egg to the second game, where it will hatch shiny. It cannot ever hatch shiny on the game that receives the egg. There's a code to stop it, but the code doesn't work on a second game that receives the egg from the first. All shiny manaphy must have link trade in the description for this reason, but it will still be treated as a hack on GTS and for wifi battle recording, despite that it was gotten legitimately in the game.