Well first of all defeat the Elite 4(including Cynthia). Then about a week later go to Pastoria city and talk to a lady(Sorry I forgot which one. Maybe just talk to everyone in town to make sure) and she will say, "Hey! Aren't you [insertname], the one who defeated the Elite 4 Well theres a man in green at the Pokemart. He says he's got something for you." Then go to the Pokemart and a man in green should be there. He will give you an Azure Flute(Used to get Arceus at the place you got Dialga). After that every time you enter a Pokemart he will be there giving you an Azure Flute. Then about a week or two later, enter a Pokemart with an empty space in your party. Talk to the man in green and he should give you a Manaphy egg! Although, like the Azure Flute, every time you talk to him he should give you a Manaphy egg, Hope this helped!